Maize streak virus-resistant transgenic maize: a first for Africa

In this article, we report transgene-derived resistance in maize to the severe pathogen maize streak virus (MSV). The mutated MSV replication-associated protein gene that was used to transform maize showed stable expression to the fourth generation. Transgenic T₂ and T₃ plants displayed a significant delay in symptom development, a decrease in symptom severity and higher survival rates than non-transgenic plants after MSV challenge, as did a transgenic hybrid made by crossing T₂ Hi-II with the widely grown, commercial, highly MSV-susceptible, white maize genotype WM3. To the best of our knowledge, this is the first maize to be developed with transgenic MSV resistance and the first all-African-produced genetically modified crop plant.     

The selection of virus-resistant Chinese hamster ovary cells.

We have selected Chinese hamster ovary (CHO) cells resistant to infection by encephalomycarditis (EMC) virus. Thus far, we have obtained five lines resistant to EMC, all of which manifest different phenotypes. Three of the five are not persistently infected with virus, while two lines produce infectious virus and grow in its presence. The nonpersistently infected lines exhibit different resistance profiles to the other viruses we have tested, and they are stable in nonselective growth conditions. Their resistance appears to be due to a genetic alteration in the cell.     

Accuracy of genomic selection in European maize elite breeding populations

Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3–4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.     

Evaluation of genome-wide selection efficiency in maize nested association mapping populations

In comparison to conventional marker-assisted selection (MAS), which utilizes only a subset of genetic markers associated with a trait to predict breeding values (BVs), genome-wide selection (GWS) improves prediction accuracies by incorporating all markers into a model simultaneously. This strategy avoids risks of missing quantitative trait loci (QTL) with small effects. Here, we evaluated the accuracy of prediction for three corn flowering traits days to silking, days to anthesis, and anthesis-silking interval with GWS based on cross-validation experiments using a large data set of 25 nested association mapping populations in maize (Zea mays). We found that GWS via ridge regression-best linear unbiased prediction (RR-BLUP) gave significantly higher predictions compared to MAS utilizing composite interval mapping (CIM). The CIM method may be selected over multiple linear regression to decrease over-estimations of the efficiency of GWS over a MAS strategy. The RR-BLUP method was the preferred method for estimating marker effects in GWS with prediction accuracies comparable to or greater than BayesA and BayesB. The accuracy with RR-BLUP increased with training sample proportion, marker density, and heritability until it reached a plateau. In general, gains in accuracy with RR-BLUP over CIM increased with decreases of these factors. Compared to training sample proportion, the accuracy of prediction with RR-BLUP was relatively insensitive to marker density.     

Non-additive gene effects in populations under different methods of selection

Summary The genetic parameters of two quantitative traits, 13-day larval weight and pupal weight, in Tribolium populations developed by reciprocal recurrent selection (RRS) and by within-line purebred selection (WLS) were compared each with the other and also with the parameters of the unselected base populations using the genetic model of Carbonell, Nyquist and Bell. The variability for two and three-way crosses of inbred lines derived from companion populations (two strains, breeds, or varieties used for a terminal cross or hybrid) was analyzed into genetic effects: autosomal additivity (^* g), autosomal heterosis (^* s), sex-linked additivity (L), sex-linked heterosis (LL), general maternal (m), specific maternal or reciprocal (r), additive by additive epistasis (aa), and deviations from the model due, among other causes, to higher order epistasis (dev). One series of crosses involved companion populations with diverse origins. For contrast, a second series of crosses involved companion populations originating from a common heterogenous base population. For the heterotic trait larval weight, ^* g and ^* s effects were equally important and accounted for over 50% of the total variation. The aa epistasis contributed another 20% and was followed in importance by higher order epistasis and general maternal effects. For the more highly heritable trait, pupal weight, ^* g effects were most important with ^* s, aa, and m effects having smaller but significant influences. Sex-linked and reciprocal effects were statistically significant for many crosses, but they were relatively unimportant overall. In general, the unselected base populations showed higher ^* g variation than either RRS or WLS populations with the reverse true for ^* s effects. In agreement with theoretical expectations, RRS was more effective than WLS in exploiting ^* s effects. The aa epistatic effects for larval weight were of major importance in the unselected populations, but RRS and WLS did not differ significantly for exploiting superior aa gene combinations. Companion populations with diverse origins revealed significantly larger variation due to ^* g and ^* s effects in crosses than did populations initiated from a common heterogeneous base.Journal Paper No. 11559 from Purdue University Agricultural Experimental Station     

Ustilago maydis populations tracked maize through domestication and cultivation in the Americas

The domestication of crops and the development of agricultural societies not only brought about major changes in human interactions with the environment but also in plants' interactions with the diseases that challenge them. We evaluated the impact of the domestication of maize from teosinte and the widespread cultivation of maize on the historical demography of Ustilago maydis, a fungal pathogen of maize. To determine the evolutionary response of the pathogen's populations, we obtained multilocus genotypes for 1088 U. maydis diploid individuals from two teosinte subspecies in Mexico and from maize in Mexico and throughout the Americas. Results identified five major U. maydis populations: two in Mexico; two in South America; and one in the United States. The two populations in Mexico diverged from the other populations at times comparable to those for the domestication of maize at 6000-10000 years before present. Maize domestication and agriculture enforced sweeping changes in U. maydis populations such that the standing variation in extant pathogen populations reflects evolution only since the time of the crop's domestication.     

RNA and protein components of maize streak and cassava latent viruses

Polyacrylamide gel electrophoresis indicated that maize streak (MSV) and cassava latent (CLV) viruses each contain one species of protein and two of RNA. The estimated protein mol. wt is 28000 for MSV and 34000 for CLV. The mol. wts obtained for the two RNA species using formamide-containing gels were the same for the two viruses: 17×10⁸ and 1–3 × 10⁶. It is suggested that the viruses have a two-part genome and that the tendency of their nucleoprotein particles to form pairs favours the delivery of complete genomes to sites of infection.     

Intercrops, Cicadulina spp., and maize streak virus disease

Intercrops of bean and finger millet were tested as a possible means of controlling maize streak virus disease (MSVD) in maize by disrupting the mating behaviour of the insect vectors of the maize streak virus, Cicadulina mbila and C. storeyi. A series of three trials were done. In the first, MSVD incidence 2 months after sowing was reduced to 14.9% and 17.4% in millet and bean intercrops compared to 29.5% in the pure maize stand. The number of male Cicadulina spp. caught on sticky pole traps was also significantly reduced relative to the control, but there was little effect on the catch of females. There was no significant yield penalty for the millet intercrop but maize yield was 49% lower in the bean intercrop treatment than in the pure stand. In the second trial, there were two millet and two bean intercrop treatments and a maize only control. Fewer male Cicadulina spp. were caught in the intercrop treatments relative to the control but MSVD incidence was reduced in one millet intercrop treatment only for which the associated maize yield penalty was 89%. In the final trial the bean intercrop was again tested but it had no effect on MSVD incidence. These experiments demonstrated that intercropping maize with bean or millet decreased vector activity and/or vector numbers. Vector catches were predominantly male, and catches of males but not females were reduced in the intercrop treatments compared with pure stands. However the lower vector catch was not consistently associated with a significant reduction in MSVD incidence, and when it was there was often an associated yield penalty in the maize due to the intercrop.     

Genetic drift and selection effects of modified recurrent full-sib selection programs in two F2 populations of European flint maize

Selection response of a modified recurrent full-sib (FS) selection scheme conducted in two European flint F₂ maize (Zea mays L.) populations was re-evaluated. Our objectives were to (1) determine the selection response for per se and testcross performance in both populations and (2) separate genetic effects due to selection from those due to random genetic drift. Modified recurrent FS selection was conducted at three locations using an effective population size N _e = 32 and a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme. Selection response was assessed using a population diallel including the source population and advanced selection cycles, as well as testcrosses with unrelatesd inbred line testers and the parental F₁ generation. Selection response per cycle was significant for grain yield and grain moisture in both populations. Effects of random genetic drift caused only a small reduction in the selection response. No significant selection response was observed for testcrosses, suggesting that for heterotic traits, such as grain yield, a high frequency of favorable alleles in the elite tester masked the effects of genes segregating in the populations. We conclude that our modified recurrent FS selection is an alternative to other commonly applied intrapopulation recurrent selection schemes, and some of its features may also be useful for increasing the efficiency of interpopulation recurrent selection programs.     

Genetically idiosyncratic responses of Drosophila melanogaster populations to selection for improved learning ability

To what extent is adaptive evolution over short timescales repeatable? To address this question, we studied the performance of crosses between replicate Drosophila melanogaster lines previously subject to selection for improved learning response in the context of oviposition substrate choice. Of the 10 pairwise F₁ crosses among the five selection lines, four performed in the original learning assay similarly to the parental lines, whereas the remaining six showed learning scores significantly below the average of the parental lines. In particular, four F₁ crosses (three involving the same line) showed no detectable learning, on a par with unselected control lines. This indicates that the response to selection in some lines involved allelic substitutions at different loci. Additional assays of crosses between two selection lines indicated that the loss of performance in hybrids generalized to another type of learning assay, and held for both short‐ and long‐term memory. Joint analysis of first‐ and second‐generation crosses between these two lines supported the hypothesis that the response to selection in these different lines was based on the spread of recessive alleles at different loci. These results show that the evolutionary trajectories of populations of the same origin subject to uniform selection may sometimes diverge over very short evolutionary timescales.     

Purification of maize streak virus and its relationship to viruses associated with streak diseases of sugar cane and Panicum maximum

Maize streak virus (MSV) was purified by homogenising infected leaf tissue in 0·01 m pH 3·9 phosphate buffer and clarifying the extract with n-butanol (7 ml/100 ml extract). Purified preparations contained particles 20 nm in diameter, some occurring singly, but most occurring in pairs, forming structures of 30 × 20 nm. The sedimentation coefficients of single and paired particles were 54 and 76 S respectively. When centrifuged in sucrose density gradients preparations made by extracting leaves at pH 3·9 gave a single intense light-scattering zone containing paired particles. Preparations made at pH 5·9 or 7·9 gave one or two additional upper zones containing single particles and fragmented material. Preparations treated with 0·05 or 0·1 m ethylene diamine tetra-acetic acid, disodium salt, (EDTA) contained no paired particles, few single particles and much fragmented material. In immunoelectrophoresis, the major component in preparations without EDTA migrated to the cathode whereas that in EDTA-treated preparations migrated to the anode. Virus isolates from streak-diseased sugarcane and guinea grass (Panicum maximum) were serologically related to MSV and had similar particles with identical sedimentation coefficients. No such particles were seen in purified preparations of healthy maize, sugarcane, or guinea grass. The viruses from sugarcane and guinea grass are probably host-adapted and are referred to correctly as the sugarcane and guinea grass strains of MSV. MSV probably contains single-stranded RNA, and the cryptogram is (R)/1:*/*:S/S:S/Au.     

The effectiveness of selection for the DNA markers of quantitative trait loci in maize populations

DNA-markers of some agronomically valuable quantitative trait loci were detected by SSR- and ISSR-PCR. Method of genetic improvement of initial population for polygenic trait complex is proposed basing on direct selection of plants according to their genotype marker profiles. Experimental modelling of marker selection within populations (gamma K26 x Mo17) F3-F4 has been carried out. Requirements of marker combination in test systems and criteria of marker informativity have been grounded. Significant effectiveness of marker selection in comparison with traditional methods of selection in maize breeding has been demonstrated.     

Genetic analysis of resistance to six virus diseases in a multiple virus-resistant maize inbred line

Key message

Novel and previously known resistance loci for six phylogenetically diverse viruses were tightly clustered on chromosomes 2, 3, 6 and 10 in the multiply virus-resistant maize inbred line, Oh1VI.

Abstract

Virus diseases in maize can cause severe yield reductions that threaten crop production and food supplies in some regions of the world. Genetic resistance to different viruses has been characterized in maize populations in diverse environments using different screening techniques, and resistance loci have been mapped to all maize chromosomes. The maize inbred line, Oh1VI, is resistant to at least ten viruses, including viruses in five different families. To determine the genes and inheritance mechanisms responsible for the multiple virus resistance in this line, F₁ hybrids, F₂ progeny and a recombinant inbred line (RIL) population derived from a cross of Oh1VI and the virus-susceptible inbred line Oh28 were evaluated. Progeny were screened for their responses to Maize dwarf mosaic virus, Sugarcane mosaic virus, Wheat streak mosaic virus, Maize chlorotic dwarf virus, Maize fine streak virus, and Maize mosaic virus. Depending on the virus, dominant, recessive, or additive gene effects were responsible for the resistance observed in F₁ plants. One to three gene models explained the observed segregation of resistance in the F₂ generation for all six viruses. Composite interval mapping in the RIL population identified 17 resistance QTLs associated with the six viruses. Of these, 15 were clustered in specific regions of chr. 2, 3, 6, and 10. It is unknown whether these QTL clusters contain single or multiple virus resistance genes, but the coupling phase linkage of genes conferring resistance to multiple virus diseases in this population could facilitate breeding efforts to develop multi-virus resistant crops.     

Accuracy of genomic selection to predict maize single-crosses obtained through different mating designs

Key message

Testcross is the worst mating design to use as a training set to predict maize single-crosses that would be obtained through full diallel or North Carolina design II.

Abstract

Even though many papers have been published about genomic prediction (GP) in maize, the best mating design to build the training population has not been defined yet. Such design must maximize the accuracy given constraints on costs and on the logistics of the crosses to be made. Hence, the aims of this work were: (1) empirically evaluate the effect of the mating designs, used as training set, on genomic selection to predict maize single-crosses obtained through full diallel and North Carolina design II, (2) and identify the possibility of reducing the number of crosses and parents to compose these training sets. Our results suggest that testcross is the worst mating design to use as a training set to predict maize single-crosses that would be obtained through full diallel or North Carolina design II. Moreover, North Carolina design II is the best training set to predict hybrids taken from full diallel. However, hybrids from full diallel and North Carolina design II can be well predicted using optimized training sets, which also allow reducing the total number of crosses to be made. Nevertheless, the number of parents and the crosses per parent in the training sets should be maximized.

     

Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations

Population and quantitative genetic models provide useful approximations to predict long-term selection responses sustaining phenotypic shifts, and underlying multilocus adaptive dynamics. Valid across a broad range of parameters, their use for understanding the adaptive dynamics of small selfing populations undergoing strong selection intensity (thereafter High Drift-High selection regime, HDHS) remains to be explored. Saclay Divergent Selection Experiments (DSEs) on maize flowering time provide an interesting example of populations evolving under HDHS, with significant selection responses over 20 generations in two directions. We combined experimental data from Saclay DSEs, forward individual-based simulations, and theoretical predictions to dissect the evolutionary mechanisms at play in the observed selection responses. We asked two main questions: How do mutations arise, spread, and reach fixation in populations evolving under HDHS? How does the interplay between drift and selection influence observed phenotypic shifts? We showed that the long-lasting response to selection in small populations is due to the rapid fixation of mutations occurring during the generations of selection. Among fixed mutations, we also found a clear signal of enrichment for beneficial mutations revealing a limited cost of selection. Both environmental stochasticity and variation in selection coefficients likely contributed to exacerbate mutational effects, thereby facilitating selection grasp and fixation of small-effect mutations. Together our results highlight that despite a small number of polymorphic loci expected under HDHS, adaptive variation is continuously fueled by a vast mutational target. We discuss our results in the context of breeding and long-term survival of small selfing populations.     

Unmasking potential intracellular roles for dysferlin through improved immunolabeling methods

Mutations in the DYSF gene that severely reduce the levels of the protein dysferlin are implicated in muscle-wasting syndromes known as dysferlinopathies. Although studies of its function in skeletal muscle have focused on its potential role in repairing the plasma membrane, dysferlin has also been found, albeit inconsistently, in the sarcoplasm of muscle fibers. The aim of this article is to study the localization of dysferlin in skeletal muscle through optimized immunolabeling methods. We studied the localization of dysferlin in control rat skeletal muscle using several different methods of tissue collection and subsequent immunolabeling. We then applied our optimized immunolabeling methods on human cadaveric muscle, control and dystrophic human muscle biopsies, and control and dysferlin-deficient mouse muscle. Our data suggest that dysferlin is present in a reticulum of the sarcoplasm, similar but not identical to those containing the dihydropyridine receptors and distinct from the distribution of the sarcolemmal protein dystrophin. Our data illustrate the importance of tissue fixation and antigen unmasking for proper immunolocalization of dysferlin. They suggest that dysferlin has an important function in the internal membrane systems of skeletal muscle, involved in calcium homeostasis and excitation-contraction coupling.     

Structure and temporal dynamics of populations within wheat streak mosaic virus isolates

Variation within the Type and Sidney 81 strains of wheat streak mosaic virus was assessed by single-strand conformation polymorphism (SSCP) analysis and confirmed by nucleotide sequencing. Limiting-dilution subisolates (LDSIs) of each strain were evaluated for polymorphism in the P1, P3, NIa, and CP cistrons. Different SSCP patterns among LDSIs of a strain were associated with single-nucleotide substitutions. Sidney 81 LDSI-S10 was used as founding inoculum to establish three lineages each in wheat, corn, and barley. The P1, HC-Pro, P3, CI, NIa, NIb, and CP cistrons of LDSI-S10 and each lineage at passages 1, 3, 6, and 9 were evaluated for polymorphism. By passage 9, each lineage differed in consensus sequence from LDSI-S10. The majority of substitutions occurred within NIa and CP, although at least one change occurred in each cistron except HC-Pro and P3. Most consensus sequence changes among lineages were independent, with substitutions accumulating over time. However, LDSI-S10 bore a variant nucleotide (G(6016)) in NIa that was restored to A(6016) in eight of nine lineages by passage 6. This near-global reversion is most easily explained by selection. Examination of nonconsensus variation revealed a pool of unique substitutions (singletons) that remained constant in frequency during passage, regardless of the host species examined. These results suggest that mutations arising by viral polymerase error are generated at a constant rate but that most newly generated mutants are sequestered in virions and do not serve as replication templates. Thus, a substantial fraction of variation generated is static and has yet to be tested for relative fitness. In contrast, nonsingleton variation increased upon passage, suggesting that some mutants do serve as replication templates and may become established in a population. Replicated mutants may or may not rise to prominence to become the consensus sequence in a lineage, with the fate of any particular mutant subject to selection and stochastic processes such as genetic drift and population growth factors.