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.

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.

Progress made in the in situ gynogenesis technique since 1990 now allows production of a high number of maize (Zea mays L.) doubled-haploid (DH) lines. The aim of the study was to compare DH lines versus selfing lines for testcross performance. DH and single-seed descent (SSD) lines were produced from random S-1 progenies of a broad-base population. For grain yield, kernel moisture, plant height, ear height and leaf length, the three population means were similar. Except for kernel moisture, the genetic variance of DH lines was nearly twice as high as the genetic variance of S-1 families, as expected. On the other hand, genetic variance among SSD lines was only 1.5 times higher than the genetic variance of S-1 families. This lower variance could be due to a selection bias in the method of production of SSD lines. However, for all traits, heritability of SSD or DH lines was higher than heritability of S-1 families. Epistasis effects in DH progenies were not significant. The consequence was a high correlation between S-1 testcross progenies and DH or SSD testcross progenies, meaning that the S-1 testcross value can be used to select the best families from which DH lines will be extracted. As a whole, the observed variation in DH lines appeared to be more in accordance with the observed variation among S-1 families than with the observed variation among SSD lines.

Theoretically, in a recurrent selection program, the use of doubled haploids (DH) can increase genetic advance per unit of time. To evaluate the efficiency expected from the use of DH for the improvement of grain yield in a maize (Zea mays L.) population, two recurrent selection programs for testcross performance were initiated using testcross progenies from DH lines and S-1 families. In 4 years one selection cycle using DH and two selection cycles using S-1 families were carried out with the same selection intensity for both methods. As expected, testcross genetic variance was twice as high among DH lines as among S-1 families. The predicted genetic gain was 8.2% for the DH selection cycle, and 10.6% for the two S-1 selection cycles, giving a per year advantage of 29% for the S-1 family method over the DH method with a cycle of 4 years. With a 3-year cycle for the DH method, both methods were expected to be equivalent. Using a tester related to the one used for selection, the genetic gains obtained were equivalent for both methods: 6.6% for the DH cycle and 7.0% for the two S-1 cycles. With a 3-year cycle for the DH method, the advantage would have been in favor of DH method. Furthermore, the DH method has the advantage of simultaneously producing lines that are directly usable as parents of a hybrid. Thus, if the genetic advance per unit of time is evaluated at the level of developed varieties even with the same or with a lower genetic advance in population improvement, the DH method appears to be the most efficient.

Nowadays development of varieties with a better nitrogen use efficiency (NUE, i.e. grain yield per unit of nitrogen from soil including fertilizer) is becoming a necessity both to allow the maintenance of a Sufficient profit margin for the farmer and to preserve ground water from nitrate pollution. A new breeding aim Could be to develop varieties adapted to low N-input. Many studies show, a genetic variability for NUE at a given level of nitrogen fertilization, with a significant genotype x nitrogen fertilization (GxN,) interaction. Such an interaction is relatively low, as illustrated by a highly significant phenotypic or genotypic correlation between yields at low and high N-input when the yield reduction at low N-input is not greater than about 35%. However, genetic variation is expressed differently at low and high N-input. Variation in NUE at high N-input is mainly related to variation in N-uptake, whereas at low N-input, both components of NUE could play a role, specifically nitrogen utilization efficiency, i.e. grain yield/N-uptake. GxN interaction for grain yield appears to be due to GxN interaction for kernel number. To have a good NUE at low N-input, it is necessary to reduce kernel abortion just after fertilization. Genotypes with a short anthesis-silking interval and prolific genotypes seem to have the ability to remobilize N from the stover to the grain efficiently, particularly in the early stage of embryo development, avoiding embryo or ear abortion. Leaf area duration appears to he in important factor for post-silking N-uptake and thus grain filling and is favourable for NUE whatever the N input. Remobilization also plays an important role at low N-input. Results from QTL detection tend to confirm that genetic variation is expressed differently at low and high N-input. Selection experiments show that to have the maximum genetic advance at low N-input, it is better to select in this N condition. Finally it appears to be quite possible to develop new varieties better adapted to low N-input than present varieties.

The paper suggests the use of graphical models as a powerful and sometimes natural tool for analysing plant genetic data. After a short review of some basic concepts of the theory of statistical graphical models, a sequence of simple hypothetical scenarios are discussed, illustrating how graphical models can be used to model many types of genetic data.

Molecular markers allow breeders to infer the genotypic value from the marker genotype, and to monitor the accumulation of favourable genes or chromosome segments (QTAs, for alleles at a QTL) in one genotype. In this synthesis, we consider three main applications with theoretical and experimental results: 1) the backcross for several QTAs, 2) different modalities of marker-assisted recurrent selection (mainly selection on markers only and combined selection on markers and phenotype), and 3) marker-assisted recurrent genotype building, genotype building being defined as the accumulation of favourable QTAs in one genotype, monitored by markers. Some possible consequences of the development of genomics are discussed. Genomics makes it possible to have direct markers of QTLs, without the risk of recombination between the marker and the QTL. This will greatly increase the efficiency of all schemes considered. It is concluded that selection and varietal development increasingly evolve towards genotype building.

A recurrent selection scheme based on combined S-1, HS and TC progeny evaluation is proposed. This scheme allows for determining population line value, GCA and SCA and provides early testing for the So genotype. Furthermore it allows for studying the intrapopulation variation of the inbreeding effect and the heterotic response. It also allows for selection under both stressed and nonstressed environments. Thus it could be integrated with commercial hybrid breeding programs. After one cycle of selection under stressed and nonstressed condition for nitrate input the scheme was effective whereas under low temperature stress at planting and early growth and high at reproductive stage it was not particularly effective.

Understanding the genetic basis of heterosis in a given species is a major issue for both evolutionary research and applied purposes. In order to map QTLs involved in heterosis in maize and to estimate their effect, we evaluated the hybrids between three connected RIL populations and the three initial parental inbreds, yielding a total of 1278 hybrids. A specific data analysis approach using multilocus models was developed using MCQTL software. Thirteen regions with significant effect on variation were detected for grain yield and 11 for grain moisture at harvest. These two traits display different genetic effects: only few significant dominance effects could be detected for moisture, whereas all yield QTLs displayed such effects. Furthermore, most yield QTLs displayed apparent overdominance effects.

Marker-assisted selection (MAS) has received extensive attention in the past ten years. Two main strategies of MAS have been proposed: the use of markers to control the introgression of gene or QTL (quantitative trait locus), and the use of markers to predict breeding values in a population under selection, Theoretical and experimental results published on the interest of these two strategies are presented, focusing on the preliminary results of a MAS experiment performed on a maize population. From these results it appears that markers can be very efficient to quickly fix favorable alleles at target genes. Nevertheless, potential interactions between QTL (or genes) and environmental conditions or genetic background can reduce the efficiency of MAS. Further work is needed to optimize the use of markers in selection.

Attempts to make sense of the inheritance of quantitative traits are now just 100 years old following the rediscovery of Mendel's work. Fisher's 1918 paper provided the springboard for most subsequent analyses, with a great expansion of interest, particularly driven by agriculture, after the second, world war. However, until the cheap availability of molecular markers in the 1990s, the whole edifice was a black box with almost no detailed knowledge of the individual genes underlying quantitative traits.This paper will provide a very 'broad brush' coverage of what the author believes to be the main conclusions relevant to plant breeding to emerge from quantitative genetics in the last 50 years. This includes the problems of identifying and interpreting genetical differences, particularly in early generation material, heterosis, gene number and the possible role of mutation.

A. prerequisite for any successful hybrid breeding program is the existence of genetically diverse gene pools. As a long time perspective for hybrid oilseed rape breeding the utilization of artificially resynthesized rapeseed could be of interest. Hybrid performance and heterosis in a series of testcrosses between resynthesized lines and the spring rapeseed cultivar 'Korall' in male sterile form were investigated under field conditions for two years at two locations in Sweden and Denmark. Genetic distances of these resynthesized lines to 'Korall' were estimated based on 47 probe/enzyme combinations resulting in 354 different bands. An average midparent heterosis of 41% for seed yield was estimated. Genetic distance was significantly correlated with leaf dry matter of four week old plants, but there was no significant correlation between seed yield and genetic distance.

In most studies done in different species, the correlation between heterosis for a given trait and the genetic distance based on molecular markers is weak. This could be due to the use of anonymous markers (i.e. not linked to genes controlling heterosis) for the estimation of the genetic distance. In the present study, we propose an algorithm to select, from a set of molecular markers, the subset that provides the genetic distance the most correlated with heterosis. Used on wheat hybrids data, this program showed its efficiency to improve the correlation. The possibilities of practical use of the program are discussed. The correlations were ir;sufficient to allow prediction of heterosis. However, this method can be used to detect genetic regions influencing heterosis and could provide useful information for a better understanding of the genetic basis of heterosis.

The paper presents some analytic and numerical comparisons of estimators of the additive gene action effect based on phenotypic observations and on molecular marker data. The analytic part shows conditions under which the two methods can be compared. The numerical results indicate that the method which uses marker genotypes underestimates the total additive effect.

Probability of success and its ratio to resource investment are introduced for the optimization of multi-step yield screening (MSS) procedures for a relatively small population of test varieties. Numerical calculations are made to determine the difference of three patterns (I, II and III) of MSS. In pattern I which has been assumed in the traditional screening theories, a specifically allocated upper fraction of the test varieties is selected in each step, and in patterns II and III, varieties superior to a check variety and a critical fixed yield value, respectively, are selected in each step. It is shown that, while pattern I MSS is useful in yield competition trials of highly promising varieties, pattern II or III MSS of single to three steps, will be efficient in preliminary yield trials. Pattern III with an appropriate critical yield value will give much better results than II.

The efficiency of molecular markers to improve genetic prediction has been proved by many studies. Nevertheless, the additional cost due to marker genotyping is seldom considered in the comparison between marker-assisted selection (MAS) and phenotypic selection. In the context of plant breeding, the relative cost efficiency of MAS in the first cycle of selection is evaluated through an analytical approach taking into account the effect of the experimental design (population size, number of trials, and replications per trial) on quantitative trait loci (QTL) detection. The same global cost is assumed for both methods. In a first step, the optimal allocation of the experimental resources is studied for each method before comparing them at their optimum. For traits sensitive to genotype x environment interactions, unreplicated trials are optimal for both methods but the optimal number of trials is different. It increases with the investment for phenotypic selection while it becomes nearly equal to one for MAS. The loss of efficiency due to non-optimal designs is evaluated. The expected economic return of MAS compared with phenotypic selection decreases with the cost of genotyping. When this cost is high, MAS interest is limited to traits with a low heritability, provided that the investment is high enough to evaluate a large population size, which is the necessary condition to explain with markers a large part of genetic variation. The maximal genotyping cost that is acceptable for MAS to be efficient is given for different values of investment and trait heritability.

To avoid pollution by nitrates and to maintain a sufficient net income, the farmer must optimize the use of nitrogen fertilizer. Using Varieties with a better nitrogen use efficiency (NUE) is a way Co reach such an objective. To study the genetic variability and genetic basis of NUE in maize(Zea mays L.) a set of 99 recombinant inbred lines crossed to a rester was studied for grain yield and other traits, including N content, in comparison to commercial varieties, at low input (N-) and high input (N+), during two years in one location. From N+ to N- grain yield was reduced by 38%, kernel number by 32% and kernel weight by 9%. Vegetative development was reduced by 14% whereas the growth after anthesis was reduced by 21%. N uptake efficiency (NUpE) was reduced by 35% at harvest whereas N utilization efficiency (NUtE) was increased by 27%. Genotype x nitrogen (G x N) interaction variance was significant for yield and kernel number, brit not for kernel weight. G x N interaction for kernel number was highly correlated to the interaction observed for yield. Responsiveness for yield or kernel number was negatively correlated to yield in N-. Heritability was decreased in N-. Differences in grain yield were easier to explain in N- than in N+. Vegetative development was favourable in both N conditions. In N-, N uptake and nitrogen nutrition index at silking were positively correlated to grain yield whereas leaf senescence and anther-silking interval were negatively correlated. NUE was explained both by NUpE and NUtE. However NUpE was more variable in N+ than in N- and the reverse for NUtE. Limiting steps in N metabolism appears to be different at low and high levels of N fertilizer.