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Heterosis, i.e., the superiority of hybrids over parental lines, is sizable for allogamous species, especially maize (Zea mays L.). Heterosis has been extensively exploited but, despite a century of investigations, its genetic basis is not completely understood, yet. To gain information on its genetic control, we undertook a long term research in maize, aimed at providing a framework of comprehensive quantitative trait locus (QTL) phenotyping, to be integrated with map based cloning. As a first step, we jointly applied classical genetic and QTL analysis in a set of recombinant inbred lines (RILs), derived from the heterotic single cross B73 × H99. RILs were crossed to the three testers B73, H99 and B73 × H99, following a North Carolina III (NCIII) mating design and testcrosses were evaluated, together with the RILs, in three environments. Level of heterosis for several agronomic traits and underlying genetic effects (allelic and non-allelic interactions) were estimated. Several QTL with heterotic effects on agronomic traits were detected and most of them were characterized by dominant or overdominant gene action, whereas non-allelic interaction proved to be of minor importance. We then developed genetic materials suitable for validation and precise estimate of the effects of six heterotic QTL chosen for their appreciable additive and dominance effects. For this purpose, we adopted a residual heterozygous lines (RHL)-based introgression program to produce pairs of near-isogenic lines (NILs) homozygous either for one or the other parental inbred allele (i.e. B73 or H99) at the selected heterotic QTL regions. In addition, during the process of NILs production, we were able to preliminarily validate the phenotypic effects of two major QTL for heterosis, mapped on chromosome 3 (bin 05) and 4 (bin 10). Once NILs were obtained, we then approached a study aimed at verifying and characterizing QTL heterotic effects. The six pairs of NILs were crossed with the two parental inbred lines B73 and H99. The 24 testcrosses are now being evaluated in a multi-year research conducted over several environments at low and high plant densities (4.5 and 9.0 plants m-2, respectively). This investigation is warranted because, in several studies, the level of heterosis has proven to be particularly important in coping with environmental stress. Results obtained in the first year of testing allowed us to confirm additive and dominance effects of heterotic QTL for traits that showed strong heterosis in our previous studies. From non-stress to stress condition, for yield per plant and other agronomic traits the contribution of additive effects declined, while that of dominance increased. These preliminary findings thus confirm the importance of heterosis in coping with stress and its possible role in enhancing crop sustainability. The ultimate objective of QTL mapping is to identify the causal genes that underlie these QTL. Starting from F1 hybrids obtained by crossing contrasting NILs, we produced large F2 populations, each segregating only for one QTL region. We limited our attention to the introgressed QTL mapped on chromosome 4 (bin 10) and 10 (bin 03) because of their sizable effects on yield and other traits. F2 populations were genotyped at markers flanking the segregating QTL, and F3 families are now being produced by selfing informative recombinant F2 individuals. The so obtained F3 families will be evaluated for agronomic traits in order to fine map the heterotic QTL.

Mapping genetics fators affecting heterosis in maize Elisabetta Frascaroli*, Maria Angela Canè*, Pierangelo Landi*, Giorgio Pea†, Michele Morgante‡, Mario Enrico Pè† * Dipartimento di Scienze e Tecnologie Agroambientali, Università di Bologna, Bologna, Italy † Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy ‡ Dipartimento di Scienze Agrarie ed Ambientali, Università di Udine, and Istituto di Genomica Applicata Parco Scientifico e Tecnologico di Udine "Luigi Danieli", Udine, Italy Abstract The term heterosis describes the superiority of heterozygous genotypes for one or more characteristics in comparison with the corresponding parental homozygotes. The higher productivity of the heterozygotes is exploited through the development of hybrid varieties in several crop species, and historically it represented one of the most outstanding advancement in plant improvement. Despite the long history of successes, especially in maize (Zea mays L.), the genetic bases of heterosis are not well understood yet. The application of molecular markers for the dissection of the genetic basis of many quantitative traits prompted the development of different approaches for the evaluation of heterosis. Our research was conducted on the genetic material developed from the single cross between maize inbred lines H99 and B73 in order to: (i) study the level of heterosis for traits of agronomic importance; (ii) identify the genomic regions (QTL quantitative trait loci) most involved in heterosis; (iii) investigate the relationships between the level of molecular marker heterozygosity and the phenotypic performance; (iv) estimate the genetic effects involved (i.e., allelic and non-allelic interactions). Materials were the basic generations, the derived 142 recombinant inbred lines (RILs) and the three testcross populations obtained by crossing the 142 RILs to each parent and their F1. RIL population was genotyped with a total of 158 marker loci arranged in a genetic linkage map. All genotypes were field-tested in three locations. The field layout was a randomized complete block design for basic generations, and a modified split-plot design for the four populations. Least square means over locations were used for subsequent analyses. Classical genetic analises were conducted following the North Caroline Model III (NCIII) and Triple Test Cross (TTC) designs. Moreover, Composite Interval Mapping was performed to search for QTL by combining plant’s phenotypic and marker’s genotypic data. QTL analysis was conducted on testcross populations’ means and on derived datasets concerning additive and dominance effects only. Thresholds for declaring putative QTL were defined by permutations. A mixed linear model was then used to map digenic epistatic QTL. Among the examined traits, seedling weight (SW), number of kernels per plant (NK) and grain yield (GY) showed heterosis greater than 100% and dominance degree higher than one. Several QTL were identified prevailingly in the additive-dominance range, for traits with low heterosis, and prevailingly in the dominance-overdominance range for plant height (PH), SW, NK and GY. Only a few QTL with digenic epistasis were identified. Some chromosome regions presented overlaps of overdominant QTL for SW, PH, NK and GY, suggesting pleiotropic effects on the overall plant vigor.

Poster Abstract C.18

Poster Abstract – H.06

Poster Abstract - D.06

Given the importance of early cold tolerance in maize (Zea mays L.), we previously conducted a divergent selection for low (L) and high (H) cold tolerance at germination. The source population was the F2 of B73 × IABO78 single cross. Selection was first conducted as recurrent selection (four cycles) and then in inbreeding (three generations). Ten lines were finally selected for L and ten for H; these lines were then evaluated to investigate: (i) their field cold tolerance in the early autotrophic phase and the relationship with the cold tolerance expressed at emergence and in the heterotrophic phase; (ii) the inheritance of these cold tolerance traits; (iii) their agronomic performance as lines per se and as crosses; (iv) their SNP-based genetic characterization. For all cold tolerance traits, the H group of lines was superior to the L group; selection responses were often symmetric, suggesting the prevalence of additive effects. The relationship among cold tolerance traits was appreciable, suggesting a common genetic basis. Differences among testcrosses were largely due to general combining ability effects and the relationship between line per se and testcross performance was high, confirming the prevalence of additive effects. Correlated responses were also obtained for agronomic traits, the H lines being superior to L lines both per se and as crosses. For SNP-marker loci, the B73 allelic frequency was greater in the H group (61.7 %) than in L group (39.7 %). Across field trials, an H line excelled for all traits, thus proving to deserve further investigations.

Background Maize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. New tools that improve our understanding of the genetic basis of quantitative traits are needed to guide predictive crop breeding. We have produced the first balanced multi-parental population in maize, a tool that provides high diversity and dense recombination events to allow routine quantitative trait loci (QTL) mapping in maize. Results We produced 1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines. The characterization of 529 MAGIC maize lines shows that the population is a balanced, evenly differentiated mosaic of the eight founders, with mapping power and resolution strengthened by high minor allele frequencies and a fast decay of linkage disequilibrium. We show how MAGIC maize may find strong candidate genes by incorporating genome sequencing and transcriptomics data. We discuss three QTL for grain yield and three for flowering time, reporting candidate genes. Power simulations show that subsets of MAGIC maize might achieve high-power and high-definition QTL mapping. Conclusions We demonstrate MAGIC maize’s value in identifying the genetic bases of complex traits of agronomic relevance. The design of MAGIC maize allows the accumulation of sequencing and transcriptomics layers to guide the identification of candidate genes for a number of maize traits at different developmental stages. The characterization of the full MAGIC maize population will lead to higher power and definition in QTL mapping, and lay the basis for improved understanding of maize phenotypes, heterosis included. MAGIC maize is available to researchers. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0716-z) contains supplementary material, which is available to authorized users.