HighlightThe genetic variation of root system architecture in the A and B wheat genomes is described, providing the necessary knowledge ultimately to fine-tune the expression of the root system architecture.

The exploitation of heterosis is one of the most outstanding advancements in plant breeding, although its genetic basis is not well understood yet. This research was conducted on the materials arising from the maize single cross B73 3 H99 to study heterosis by procedures of classical genetic and quantitative trait loci (QTL) analyses. 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 F 1 . For seedling weight (SW), number of kernels per plant (NK), and grain yield (GY), heterosis was .100% and the average degree of dominance was .1. Epistasis was significant for SW and NK but not for GY. Several QTL were identified and in most cases they were in the additive-dominance range for traits with low heterosis and mostly in the dominance-overdominance range for plant height (PH), SW, NK, and GY. Only a few QTL with digenic epistasis were identified. The importance of dominance effects was confirmed by highly significant correlations between heterozygosity level and phenotypic performance, especially for GY. Some chromosome regions presented overlaps of overdominant QTL for SW, PH, NK, and GY, suggesting pleiotropic effects on overall plant vigor.

Association mapping provides useful insights on the genetic architecture of quantitative traits across a large number of unrelated genotypes, which in turn allows an informed choice of the lines to be crossed for a more accurate characterization of major QTLs in a biparental genetic background. In this study, seedlings of 183 durum wheat elite accessions were evaluated in order to identify QTLs for root system architecture (RSA). The QTLs identified were compared with QTLs detected for grain yield and its component traits, plant height and peduncle length measured in a previous study where the same accessions were evaluated in 15 field trials with a broad range of soil moisture availability and productivity (Maccaferri et al. in J Exp Bot 62:409–438, 2011). The following RSA features were investigated in seedlings at the four-leaf stage: seminal root angle, primary root length, total root length, average root length, root number and shoot length. Highly significant differences among accessions were detected for all traits. The highest repeatability (h2 = 0.72) was observed for seminal root angle. Out of the 48 QTLs detected for RSA, 15 overlapped with QTLs for agronomic traits and/or grain yield in two or more environments. The congruency of the effects of RSA traits and agronomic traits was evaluated. Seminal root angle and root number appear the most promising traits for further studies on the adaptive role of RSA plasticity on field performance in environments differing for water availability. Our results provide novel insights on the genetic control of RSA and its implications on field performance of durum wheat.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-014-0177-1) contains supplementary material, which is available to authorized users.

BackgroundDurum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.ResultsHigh quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman’s rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold = 0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.ConclusionsThe consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-873) contains supplementary material, which is available to authorized users.

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 x 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.

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.

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.

Irrigation treatments involving three different water regimes were carried out in a controlled environment on eight near-isogenic durum wheat lines that differed in a major yield-related QTL region (QYld.idw-3B) in order to assess the relationship between morphophysiological traits, antioxidant enzyme activities, polyamine contents and drought tolerance.Drought stress, simulated under a rain-out shelter, negatively affected the performance of the isogenic lines, leading to significant reductions in seed yield, tiller number, chlorophyll content, plant height, leaf area and ascorbate peroxidase activity, while the polyamine content and guaiacol peroxidase activity increased. Correlation analysis revealed that the antioxidant enzyme activities in the flag leaf were in significant, negative relationship with several yieldrelated parameters, while a significant, positive correlation was found between polyamine contents and the seed number or weight in the main spike. The ascorbate peroxidase activity was negatively correlated with seed weight per main (r= -0.446) or side spike (r= -0.465) and the 1000-grain weight of the main or side spike (r= -0.396 or r= -0.49) and the guaiacol peroxidase activity with the number of seeds per main (r= -0.457) or side spike (r= -0.378) and the seed weight per side spike (r= -0.38). GGE biplot analysis showed that lines with the KK 2BL KK 3BS allele combination had better yield performance under non-watered conditions, but their response to drought stress was not uniform in other yield-related traits.