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In a previous study on a maize (Zea mays L.) population of recombinant inbreds derived from B73 × H99, we identified several quantitative trait loci (QTL) for agronomic traits with high dominance-additive ratio. Then, for four of these QTL, we developed families of near-isogenic lines (NILs) homozygous either for the QTL allele from B73 (BB) or from H99 (HH); for two of these QTL, the NILs' families were produced in two different genetic backgrounds. The present study was conducted to: (1) characterize these QTL for agronomic traits and (2) verify whether their effects were influenced by the genetic background, inbreeding level and plant density (PD). The six NILs' families were tested across 3 years and in three experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two PDs (4.5 and 9.0 plants m(-2)). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance-additive ratio superior to 1 for several traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and PD were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using the NILs' families and their crosses as base materials.

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.

Summary Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi-allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd-B1, while the latter overlapped with the vernalization locus VRN-A3. Additionally, 21 QTL with environment-specific effects were found. Our results indicated a prevalence of environment-specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.

Full-sib family recurrent selection for grain yield was conducted for four cycles in maize (Zea mays L.). The source population was the F 2 of A632 (with red cob) × Mu195 (with white cob). Objectives of this research were to evaluate the change in allelic frequency at the P1 gene (determining cob color), to assess whether this change was due to random drift only, and to detect whether allelic frequencies were correlated with grain yield responses. The source and the four selected populations were crossed to two inbred lines with white cob (recessive trait). The frequency of red cob allele increased with selection following a highly significant linear trend (b = 0.066 cycle -1 ), suggesting the effect of directional selection. Correlation between allelic frequency and grain yield was significant for populations as S2 generation (r = 0.938), and as testcrosses (r = 0.886), and could be ascribed to tight linkage, to pleiotropy, or both.

Recent advances in high-throughput sequencing technologies have triggered a shift toward single-nucleotide polymorphism (SNP) markers. A systematic bias can be introduced if SNPs are ascertained in a small panel of genotypes and then used for characterizing a larger population (ascertainment bias). With the objective of evaluating a potential ascertainment bias of the Illumina MaizeSNP50 array with respect to elite European maize dent and flint inbred lines, we compared the genetic diversity among these materials based on 731 amplified fragment length polymorphisms (AFLPs), 186 simple sequence repeats (SSRs), 41,434 SNPs of the MaizeSNP50 array (SNP-A), and two subsets of it, i.e., 30,068 Panzea (SNP-P) and 11,366 Syngenta markers (SNP-S). We evaluated the bias effects on major allele frequency, allele number, gene diversity, modified Roger's distance (MRD), and on molecular variance (AMOVA). We revealed ascertainment bias in SNP-A, compared to AFLPs and SSRs. It affected especially European flint lines analyzed with markers (SNP-S) specifically developed to maximize differences among North American dent germplasm. The bias affected all genetic parameters, but did not substantially alter the relative distances between inbred lines within groups. For these reasons, we conclude that the SNP markers of the MaizeSNP50 array can be employed for breeding purposes in the investigated material. However, attention should be paid in case of comparisons between genotypes belonging to different heterotic groups. In this case, it is advisable to prefer a marker subset with potentially low ascertainment bias, like in our case the SNP-P marker set.

The early genotypes of maize (Zea mays L.) selected for the northern Corn Belt regions can perform poorly when grown as a delayed-sowing crop in warmer regions. Two early synthetics, A and B, were developed and two cycles of a modified reciprocal recurrent selection were conducted in a delayed-sowing crop by using A632 as a tester for Synthetic A and W117 as a tester for Synthetic B. Selection was based on a multitrait index involving grain yield, percent erect plants, and grain moisture. This study was conducted in three environments to evaluate the effects of selection. The source and selected populations of the two synthetics were tested per se and in hybrid combination to each other, to their inbred tester, and to the unrelated hybrid, A188 × W64A. The gain in the cross between the two synthetics was 4.9% cycle -1 (P≤0.01) for the performance index (calculated similarly to the selection index), and this was mainly due to the gain in grain yield (12.2% cycle -1 ). However, undesired increases were found for grain moisture and silking date. The gains for performance index and grain yield were due to a balanced contribution of both changes per cycle of populations per se and of heterosis. Synthetic B contributed more than Synthetic A to the gain in the population cross for performance index, grain yield, and to the loss of earliness. Population crosses of both synthetics with corresponding testers and A188 × W64A showed a positive response for performance index and grain yield, and a loss of earliness for Synthetic B. The results indicated that the selection procedure was effective in improving the performance index of the two synthetics both per se and in hybrid combinations

Improving cold tolerance in maize (Zea mays L.) is an important breeding objective, allowing early sowings which result in many agronomic advantages. Using as source the F(2) population of B73 × IABO78 single cross, we previously conducted four cycles of divergent recurrent selection for high (H) and low (L) cold tolerance level, evaluated as the difference (DG) between germination at 9.5 °C and at 25 °C in the germinator. Then, we pursued the divergent selection in inbreeding from S(1) to S(4). This research was conducted to study (1) the direct response to selection (by testing ten S(4) L and ten S(4) H lines), (2) the trait inheritance (in a complete diallel scheme involving four L and four H lines), (3) the associated responses for cold tolerance in the field (at early and delayed sowings) and (4) the responses for other traits, by testing the ten L and the ten H lines at usual sowing. Selection was effective, leading to appreciable and symmetric responses for DG. Variation among crosses was mainly due to additive effects and the ability to predict hybrid DG based on parental lines DG was appreciable. Associated responses for cold tolerance traits in the field were noticeable, though the relationship between DG and these traits was not outstanding. High tolerance was also associated with early flowering, short plants, less leaves, low kernel moisture, red and thin cob, and flint kernels. These divergently selected lines can represent valuable materials for undertaking basic studies and breeding works concerning cold tolerance.

The objectives of this research were to determine if genes controlling the reaction to the herbicide acetochlor in maize (Zea mays L.) are active during both the haploid and the diploid phases of the life cycle and if pollen selection can be utilized for improving sporophytic resistance. Pollen of eight inbred lines, previously characterized through sporophytic analysis for the level of tolerance to acetochlor, showed a differential reaction to the herbicide forin vitro tube length; moreover, such pollen reactions proved to be significantly correlated (r =0.786(*),df=6) with those of the sporophytes producing the pollen. Pollen analysis of two inbred lines (i.e. Mo17, tolerant, and B79, susceptible) and their single cross showed that thein vitro pollen-tube length reaction of the hybrid was intermediate between those of two parents. An experiment on pollen selection was then performed by growing tassels of Mo17xB79 in the presence of the herbicide. Pollen obtained from treated tassels showed a greater tolerance to acetochlor, assessed asin vitro tube length reaction, than pollen obtained from control tassels. Moreover, the backcross [B79 (Mo17xB79)] sporophytic population obtained using pollen from the treated tassels was more tolerant (as indicated by the fresh weight of plants grown in the presence of the herbicide) than was the control backcross population. The two populations did not differ when grown without the herbicide. These findings indicate that genes controlling the reaction to acetochlor in maize have haplodiploid expression; consequently, pollen selection can be applied for improving plant tolerance.

The activity of the plant inner membrane mitochondrial anion channel (PIMAC) is involved in metabolite shuttles and mitochondrial volume changes and could have a role in plant temperature tolerance. Our objectives were to in- vestigate (i) the occurrence and (ii) the temperature de- pendence of anion fluxes through PIMAC in mitochondria isolated from seedlings of three maize populations differing in terms of cold tolerance; and (iii) the relationships between the PIMAC activity kinetics and the level of cold tolerance. Populations were the source population (C0) and two populations divergently selected for high (C4H) and low (C4L) cold tolerance. Such divergently selected popula- tions are expected to share most of their genes, with the main exception of those genes controlling cold tolerance. Arrhenius plots of PIMAC chloride fluxes showed a linear temperature dependence when seedlings were grown at 25 or 14C, whereas a non-linear temperature dependence was found when seedlings were grown at 5C, with or with- out acclimation at 14C. The activation energy and other thermodynamic parameters of PIMAC activity varied depending on temperature treatments during seedling growth. When seedlings were grown at 14 and 5C with acclimation, PIMAC activity of the C4H population increased, while that of C4L declined, as compared with the activities of seedlings grown at 25C. These symmetric responses indicate that PIMAC activity changes are asso- ciated with genetically determined differences in the cold tolerance level of the investigated populations. We conclude that anion fluxes by PIMAC depend upon changes on growth temperature and are differentially related to the tolerance level of the tested populations.

Four cycles of divergent full-sib recurrent selection for the ability to germinate at low temperature were conducted in a maize (Zea mays L.) F2 population. The selection criterion was the high (H) or the low (L) value in algebraic terms of the difference (DG) between germination percentage at 9.5°C (G9.5) detected 19 days after sowing and germination percentage at 25°C (G 25) seven days after sowing; both traits were evaluated in a controlled environment (germinator). Direct and correlated responses estimated during the course of selection were in accordance with those evaluated at the end. Selection for H led to populations with higher DG values, while the reverse was noted for L; differences between H and L populations increased in successive selection cycles, though divergence tended to level off. Selection for H also resulted in higher G 9.5 (day 19), shorter germination time and more flinty kernels, while selection for L led to responses in the opposite direction as well as to a lower G 9.5 detected 37 days after sowing (i.e. at the end of germination). In contrast, responses were negligible for G 25 and varied erratically from one cycle to another for kernel weight.

Although heterosis is widely exploited in agriculture, a clear understanding of its genetic bases is still elusive. This work describes the development of maize recombinant near-isogenic lines (NILs) for the mendelization of six heterotic QTL previously identified based on a maize (Zea mays L.) RIL population. The efficient and inexpensive strategy adopted to generate sets of NILs starting from QTL-specific residual heterozygous lines (RHLs) is described and validated. In particular, we produced nine pairs of recombinant NILs for all six QTL starting from RHLs F(4:5) originally obtained during the production of the RIL population mentioned above. Whenever possible, two different NIL pairs were generated for each QTL. The efficiency of this procedure was tested by analyzing two segregating populations for two of the selected heterotic QTL for plant height, yield per plant and ears per plant. Both additive and dominant effects were observed, consistently with the presence of the QTL within the introgressed regions. Refinement of QTL detection was consistent with previous observations in terms of effects and position of the considered QTL. The genetic material developed in this work represents the starting point for QTL fine mapping aimed at understanding the genetic bases of hybrid vigor in maize.

The evaluation of recombinant inbred lines (RILs) per se can be biased by inbreeding depression in case of allogamous species. To overcome this drawback, RILs can be evaluated in combination with testers; however, testers can carry dominant alleles at the quantitative trait loci (QTL), thus hampering their detection. This study was conducted on the maize (Zea mays L.) population of 142 RILs derived from the single cross B73 × H99 to evaluate the role of different testers in affecting: (1) QTL detection, (2) the estimates of their effects, and (3) the consistency of such estimates across testers. Testcrosses (TCs) were produced by crossing RILs with inbred testers B73 [TC(B)], H99 [TC(H)], and Mo17 [TC(M)]. TCs were field tested in three environments. TC(B) mean was higher than TC(H) mean for all traits, while TC(M) mean was the highest for plant vigor traits and grain yield. As to the number of detected QTL, tester Mo17 was superior to H99 and B73 for traits with prevailing additive effects. Several overlaps among the QTL were detected in two or all the three TC populations with QTL effects being almost always consistent (same sign). For traits with prevailing dominance–overdominance effects, as grain yield, the poor performing tester H99 was clearly the most effective; fewer overlaps were found and some of them were inconsistent (different sign). Epistatic interactions were of minor importance. In conclusion, the three testers proved to affect QTL detection and estimation of their effects, especially for traits showing high dominance levels.

Molecular Breeding, 16 (4), ISSN:1380-3743, ISSN:1572-9788

Rhizobacteria (2808) were isolated on Pseudomonas-selective S1 medium from two maize inbred lines and from their hybrid at three plant growth stages. Positive phl D hybridization was found for 364 of them. The PhlD+ isolates were significantly more numerous in the rhizosphere of the hyrid than in those of parental lines. Furthermore, the frequency of PhlD+ was significantly higher for the hybrid at the flowering stage. An amplified rDNA restriction analysis showed that the hybrid genotype also increases the genetic diversity of PhlD+ populations when compared with its inbred parent lines, and this could be an effect of heterosis. Influence of the hybrid on the frequency and diversity of the bacterial PhlD+ population varied along the plant growth stage.

Pollen selection can lead to correlated responses in the subsequent sporophytes because many genes are expressed in both haploid and diploid phases. This study was conducted to evaluate the effects of pollen selection for tolerance to the herbicide alachlor [2-chloro-N-(2,6-diethylphenyl)-N-(methoxymethyl) acetamide] in maize (Zea mays L.). Tassels of the single cross hybrid K55 (tolerant) x Ky226 (susceptible) were grown in absence (control) and in presence (selected) of alachlor (1 g L -1 ). Mature pollen from this process was used to make backcrosses to Ky226 (susceptibility being recessive). The selected population outperformed the control population (88 vs. 81%; P ≤ 0.01) for percentage of normal seedlings (i.e., not injured by alachlor) when compared in a field trial treated with the herbicide (5 kg a.i. ha -1 ). Pollen of plants grown without alachlor was analyzed in vitro; in presence of the herbicide in the medium (50 mg L -1 ) the selected population exceeded the control population for pollen tube length (334 vs. 308 μm; P ≤ 0.01). Two cycles of pollen selection were also conducted in the single cross hybrid K55 x H99 (susceptible) following the backcross procedure to the susceptible parent. Seeds of control and selected populations were exposed to alachlor (1 g L -1 ), and seedlings were grown in the greenhouse. For percentage of normal seedlings, we obtained a gain (16%) in the first cycle and an additional gain (10%) in the second cycle. The results indicate that genes controlling alachlor tolerance in maize are expressed in both haploid and diploid phases and that pollen selection can be effectively applied to improve the trait.