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.A MONG the different methods that use molecular markers for selection, genomic selection (GS) has received considerable attention in the last decade. The objective of this approach is to predict the breeding values of candidates based on their molecular marker genotypes. A prediction formula is developed using the genotypes and phenotypes of reference individuals forming a calibration set (Meuwissen

BackgroundIn 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.ResultsHere, 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.ConclusionsTo 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.

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Lack of early season vigor in maize (Zea mays L.) hybrids and inbreds from the USA limits their use in places with cool humid springs. Kernel size may be related to early growth of maize. Our objectives were to estimate general combining ability (GCA), specific combining ability (SCA), and reciprocal effects (RE) for early vigor and plant growth‐related traits and to determine the relationship between these effects and those of kernel weight. Ten maize inbreds were crossed in diallel fashion, including reciprocals in two different plots. Kernel weight was recorded for each seed source for each hybrid. The 90 hybrids were evaluated for 2 yr in a split‐plot design where genotypes were the main plots and seed sources were the subplots. Traits were early vigor, plant weight, pollen and silk date, leaves below the ear, total leaf number, and plant height. Significant GCA was detected for all traits except plant weight, and SCA was significant for all traits except kernel weight. Significant RE was detected for kernel weight, early vigor, and pollen and silk date. Inbred EP42 had the highest GCA and a favorable RE for early vigor. Regression on the RE of kernel weight was significant for the RE of early vigor (R2 = 0.67), plant weight {R2 = 0.36), and pollen (R2 = 0.52) and silk date (R2 = 0.45). The inbreds producing heavier kernels should be used as seed producing parents to obtain hybrids with better early vigor and earlier flowering dates.

Adaptation of maize (Zea mays L.) to early planting dates requires the improvement of cold tolerance, which implies high percentage emergence and vigorous seedling growth under cold temperatures. The objectives of this work were to evaluate the combining ability of elite European maize inbreds for cold tolerance and to study the inheritance of cold tolerance. Five maize inbreds, differing in sensitivity to cold temperatures, were crossed by means of a diallel design. Hybrid seed was obtained at two production environments. Hybrids were planted on trays filled with sterilized peat in a cold chamber at four minimum temperatures, and these hybrids were also grown in field trials at two locations in northwestern Spain. The most cold‐tolerant inbreds, according to previous unpublished inbred evaluations in the cold chamber, F7 and EA2087, produced the most cold‐tolerant hybrids. Inbred F7 performed slightly better in hybrid combinations than EA2087 for emergence‐related traits in the cold chamber, and EA2087 was superior in hybrid combinations to F7 for seedling growth. The inbred F7 may contribute cold tolerance at emergence, whereas EA2087 contributed cold tolerance for both emergence and seedling growth. In the field, inbreds F7 and H104W were the best parent for cold‐tolerant hybrids. Percentage emergence was not related to the other traits. Generally, the genetic regulation of cold‐tolerance traits conformed to an additive‐dominance model, and it should be possible to combine both high percent emergence and vigorous seedling growth. A promising source of new cold‐tolerant inbreds is the cross between EA2087 and F7.

Genetic and phenotypic analysis of two complementary maize panels revealed an important variation for biomass yield. Flowering and biomass QTL were discovered by association mapping in both panels. 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.

15The effect of low temperature on the physiology of maize has been well studied, but the

BackgroundBreeding 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.ResultsWe 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.ConclusionsThese results open new possibilities to genetically improve cold tolerance either with genome-wide selection or with marker assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0816-2) contains supplementary material, which is available to authorized users.