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Variation for maize (Zea mays L.) kernel vitreousness is of interest in the improvement of maize for human and ruminant nutrition based on its connection with starch degradability in the rumen as well as the concentration of lysine and other essential amino acids. In this trial, 199 recombinant inbred lines (RILs) from the intermated B73 and Mo17 (IBM) population and 133 testcrosses of the IBM RIL with inbred W604S were grown in two replications in two Wisconsin locations in 2007. Ears were harvested at physiological maturity and ground kernel samples were scanned using near-infrared spectroscopy (NIRS). Samples representing the NIRS spectral range were scored for kernel vitreousness using a horizontal light box and for kernel hardness using the Stenvert hardness test. The RIL phenotypes for hardness and vitreousness followed a normal distribution, and transgressive segregation was seen for both traits. Correlations between inbreds and respective testcrosses for hardness and vitreousness were significant and positive. The correlation between hardness and vitreousness was also positive. Quantitative trait loci (QTL) analysis of this population found 33 QTL for hardness and vitreousness with several QTL overlapping across traits. The IBM population represents a good model for the study of variation of kernel vitreousness in U.S. Corn Belt Dent germplasm and the genomic regions identified could be useful for the genetic improvement of maize varieties with enhanced nutritional composition. doi: 10.2135/cropsci2009.12.0726

Wisconsin Quality Synthetic (WQS) is a maize population that has undergone four cycles of [S.sub.2]-topcross selection for increased silage yield and feed quality. This study evaluated forage yield and quality for each cycle of WQS per se as well as testcrosses to two Stiff Stalk-type testers. Linear improvement was seen in whole-plant yield, stover yield, and whole-plant quality both in the population per se and in testcrosses. Stover quality has not improved through selection. Starch content has increased while crude protein has decreased. Milk yields on a Mg dry matter and hectare basis have increased with selection. Changes in silage dry matter yield have been greater on a percent basis than changes in silage quality, suggesting that the current selection protocol of selecting [S.sub.2]-top-crosses first for yield then for quality may be more efficient at improving yield than quality. Selection directly focused on stover quality may be necessary if more rapid improvement in stover composition is desired. doi: 10.2135/cropsci20009.12.0725

Maize hybrids with improved stover yield and quality are needed to support the emerging cellulosic biofuels industry. Knowledge of the genetic variation, covariation, and genetic architecture of agronomic and cell wall traits will help maize breeders improve relevant traits through selective breeding and genetic engineering. We utilized the maize intermated B73 x Mo17 (IBM) recombinant inbred line (RIL) population to map quantitative trait loci (QTL) and to evaluate the genetic relationships among traits relevant for cellulosic biofuel production, including grain yield, stover yield, neutral detergent fiber digestibility (NDFD), and glucan, xylan, anal lignin concentration. Intermated B73 x Mo17 RIL were evaluated per se and as testcrosses to W604S to assess how well performance and QTL effects correspond between inbreds and hybrids. There were no unfavorable correlations between agronomic and cell wall traits within the testcross progeny. Polysaccharide content was either positively correlated to, or not correlated to, NDFD, indicating that increasing both carbohydrate content and convertibility is feasible. Quantitative trait loci were identified for all traits evaluated, but few QTL were in common between inbred per se and testcross evaluations despite moderate to high genotypic correlations between progeny types. This study provides information that will support the development of dual-purpose maize hybrids that are high in grain yield and also high in yield of digestible cellulosic feedstock. doi: 10.2135/cropsci2009.04.0168

The use of maize (Zea mays L.) stover as a feedstock for cellulosic biofuels production will create demand for maize hybrids with greater stover yield. It is expected that grain yield will remain the most critical trait and continue to drive hybrid sales, requiring that any increases in stover yield be made without sacrificing grain yield potential. The objective of this review was to determine the relationship between grain yield, harvest index, and stover yield to illuminate the potential for increasing both grain and stover yield through breeding. In contrast to what has been observed in other crops, gains in maize grain yield over time in the U.S. Corn Belt have been accompanied by increases in stover yield. Where recurrent selection on grain yield has been most successful, stover yield also increased while harvest index has been relatively stable. The opposite situation has been observed in tropical germplasm, where gains in grain yield have been associated with increasing harvest index and relatively constant biomass yield. We expect that stover yield of Corn Belt hybrids will continue to increase along with grain yield, resulting in future hybrids capable of producing both more food and biofeedstock for energy production. If maize breeders pursue selection for increased stover yield, we found no evidence to suggest that breeding for stover yield will necessarily reduce rate of gain in grain yield. doi: 10.2135/cropsci2009.02.0086

Maize (Zea mays L.) stover has been identified as an important feedstock for the production of cellulosic ethanol. Our objectives were to measure hybrid effect and combining ability patterns of traits related to cellulosic ethanol production, determine if germplasm and mutations used for silage production would also be beneficial for feedstock production, and examine relationships between traits that are relevant to selective breeding. We evaluated grain hybrids, germplasm bred for silage production, brown-midrib hybrids, and a leafy hybrid. Yield and composition traits were measured in four environments. There was a 53% difference in stover yield between commercial grain hybrids that were equivalent for other production-related traits. Silage germplasm may be useful for increasing stover yield and reducing lignin concentration. We found much more variation among hybrids than either in vitro ruminal fermentability or polysaccharide concentration. Correlations between traits were mostly favorable or nonexistent. Our results suggest that utilizing standing genetic variation of maize in breeding programs could substantially increase the amount of biofuels produced from stover per unit area of land.

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The open-pollinated maize (Zea mays subsp. mays) population Golden Glow [GG(MP)] provides excellent material for the study of morphological and genetic changes associated with selection for prolificacy. Late generations of the GG(MP), when planted at low densities, resemble the architecture of teosinte (Z. mays snbsp, parviglumis), the ancestor of maize. Our objectives were (i) to identify molecular markers linked to chromosomal regions that influenced prolificacy and related morphological traits, (ii) to determine whether genes previously shown to influence branching patterns in maize were associated with quantitative trait loci (QTLs) influencing these traits, and (iii) to determine whether epistatic interactions among putative QTLs influenced prolificacy and correlated traits. A mapping population was developed from the cross of inbred A679 and a highly prolific S- plant from Cycle 23 of GG(MP). Simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers were combined for the linkage map construction. Thirty-three QTLs were found for 14 of the 16 traits analyzed. A region located on Linkage Group 1 (LG 1) shared similarities with the pattern of development suggested for the teosinte branched1 (tb1) mutant. This suggests that genetic control of prolificacy and associated traits in GG(MP) may resemble the genetic changes underlying branching morphology that occurred during maize domestication. No evidence for additive-by-additive epistatic interactions was found. Abbreviations: AFLP, amplified fragment length polymorphism; CIM, composite interval mapping; cM, centimorgan; LG, linkage group; PCR. polymerase chain reaction; QTL, quantitative trait locus; SSR, simple sequence repeat; tb1, teosinte branched1., THE GENETIC BASIS underlying morphological change is the focus on much current research and it is essential to understanding evolutionary biology. It has been suggested that plant populations can undergo [...]

Prolificacy (the potential to produce ear shoots at multiple nodes on the main stalk) has been under selection since the early domestication of maize (Zea mays subsp, mays) from teosinte (Z. mays subsp. parviglumis). Until the early part of the 20th century, before mechanization, human selection may have favored single-eared maize because it facilitated hand-harvesting. Prolificacy, however, has the potential to increase stress tolerance under intensive management. Our objectives were (i) to assess variation for prolificacy and 15 related morphological traits in a population of 194 [F.sub.3] families derived from inbred line A679 and a highly prolific [S.sub.1] plant from the cultivar Golden Glow after 23 cycles of mass selection for prolificacy; and (ii) to determine relationships among traits and to infer which ones appear to be controlled by similar genetic factors. Traits were evaluated with two replications in three field environments. The population varied significantly for all traits and most traits had relatively high heritabilities (>0.80). Some traits were highly correlated, and two main groups were identified. These groups involved traits mostly associated with either the activity of axillary meristems, or intercalary meristems. In general, the correlations of trails across these two groups were insignificant or of lesser magnitude than within groups, suggesting that common genetic factors might be influencing some of these morphological traits. Abbreviations: BLUP, best linear unbiased prediction; REML, restricted maximum likelihood., MAIZE PLANTS initiate axillary meristems on most nodes of the main stalk, but many potential ear shoots abort during plant development, resulting in one or two grain-filled ears in most [...]

Maize (Zea mays L.) has the potential to produce an ear primordium at several nodes, and selection for increased prolificacy often increases grain yield. We have previously demonstrated the effectiveness of mass selection for increasing the number of active ear shoots in the `Golden Glow' maize population. The objective of our research was to evaluate associated changes in ear and plant morphology after 24 cycles of mass selection for prolificacy in Golden Glow. Cycles 0, 6, 12, 18, 23, and 24 were grown in 1997 at two locations (Madison and Arlington, WI) at two planting densities (15 070 and 73 197 plants [ha.sup.-1]). At the lower planting density, the mean number of ears per plant increased from 1.61 at C0 to 4.93 at C24, and the response rate increased over the more recent cycles, mainly from C18 to C24. At C24, tiller number has increased, and lateral branches (terminating in ears) were located at approximately one node higher and two nodes lower on the main stalk compared with the original population. Total node number on the main stalk increased, and the internode length decreased over the 24 cycles, but the opposite occurred for lateral branches. At the lower planting density, ear diameter, ear length, and kernel size decreased by 0.03, 0.10, and 0.01 cm [cycle.sup.-1] respectively, but total number of kernels per plant and dry kernel weight per plant increased significantly at a rate of 36.69 kernels [cycle.sup.-1] and 5.60 g [cycle.sup.-1] over the 24 cycles. Similar trends, but of lesser magnitude, were observed at the higher planting density. The changes in plant morphology observed across cycles of selection for prolificacy represent a general derepression of axillary meristematic growth in both main stalks and lateral branches., MAIZE HAS THE POTENTIAL to produce an ear primordium at several nodes, even though most modern hybrids have only one or two ears, at least under the conditions in which [...]

The reactive island (RI) theory of chemical reaction rates is modified so that a precise knowledge of the transition state is not required. This revised form of the theory is applied to a realistic two (J=0) and three degree of freedom model (J≠0) of the isomerization HCN⇄CNH. The detailed reaction dynamics is examined and understood in terms of the cylindrical manifolds embedded in the molecular phase space. Of special interest we find a T-shaped conformer in addition to the HCN and CNH moieties at J=0. Rates of unimolecular decay are examined by numerical simulation and theory. Good agreement is found between theory and simulation except for a case where a substantial amount of phase space is consumed by regular motion. In all cases studied, the theory is a significant improvement over the Rice–Ramsperger–Kassel–Marcus (RRKM) theory, which is up to three orders of magnitude too large. [ABSTRACT FROM AUTHOR]

In a series of recent publications we discussed the concept of cylindrical manifolds and their role in mediating the reaction dynamics of chemical reactions. The cylindrical manifolds were used to develop a chemical reaction rate theory we called reactive island (RI) theory. RI theory was cast in terms of the map dynamics between n Poincaré mapping planes—which were referred to as the ‘‘n-map.’’ Therefore ‘‘time’’ did not explicitly appear within n-map RI theory. In this paper we extend n-map RI theory to the time domain. The formal theory, cast as a master equation, is used to obtain the temporal RI model. Temporal RI theory is applied to a two degree-of-freedom system exhibiting dynamical chaos. The results of temporal RI theory are compared with classical Rice–Ramsberger–Kassel–Marcus (RRKM) theory and it is found that even under, presumably, ‘‘ideal’’ dynamical conditions, RRKM theory can be in serious error with numerical simulation. It is also seen that temporal RI theory accurately accounts for the rates at energies far above the barrier, where RRKM theory is not expected to be applicable. We also discuss some rigorous comparisons between the decay rates obtained from n-map and temporal RI theories. [ABSTRACT FROM AUTHOR]

In Paper I we discussed the existence of cylindrical manifolds embedded in phase space which mediate the dynamics of chemical reactions. A kinetic theory of population decays and decay rate constants was developed which we called ‘‘reactive island’’ (RI) theory. In this paper we discuss the details of the numerical implementation of the theory and then apply it to several molecular models (with two coupled degrees of freedom) representing isomerization between two and three states. Numerical simulations of population decays and asymptotic decay rate constants are compared to the RI theoretical predictions as well as the predictions from the Purely Random Theory (PRT) and Transition State Theory (TST) of reactions. Of the ten systems studied we find that RI theory is generally in good to excellent agreement with the numerical simulations. Only one system exhibits significant deviation between the RI and numerical results. This deviation is seen to be a result of a strong intraconformer dynamical bottleneck. Finally, we compare the theoretical prediction and the numerical simulation for the average n-map mapping time Trxn and find that the agreement, within numerical error, is exact irrespective of the character of the dynamics (i.e., chaotic or regular). [ABSTRACT FROM AUTHOR]

A microcanonical kinetic theory of reactions based upon the structure within phase space is developed. It is shown that the dynamics of reaction across an energetic barrier is mediated by invariant manifolds embedded in phase space that have the geometry of simple cylinders. The ideas are developed by considering molecular systems modeled by two vibrational degrees of freedom, a reaction coordinate and a ‘‘bath’’ coordinate. The kinetic theory is constructed by focusing on the dynamics between n mapping planes (‘‘n-map’’) and the ‘‘reactive island’’ (RI) structure within them. We discuss how the structure of the conformer population decay in isomerization reactions can be obtained from the RI kinetic model. Formal solutions of the kinetic equations are discussed with specific attention given towards the calculation of the isomerization reaction rate. The formal theory is developed in Paper I of this series. Numerical considerations and applications to the reaction dynamics of model molecular systems with two degrees of freedom will be given in Paper II and extension of the theory and applications to multidimensional systems will be given in Paper III. [ABSTRACT FROM AUTHOR]

A projection operator formalism is used to quantify the normal/resonant character of eigenstates of a vibrational Hamiltonian with two degrees of freedom. We show how the application of the formalism quantifies the resonant character of these eigenstates, in the form of a probability, and how this probability is related to the width of the resonance in classical phase space. Normal and resonant quantum numbers shared by a given eigenstate are found to be canonically related. [ABSTRACT FROM AUTHOR]

In this paper we focus on the detailed nonlinear classical dynamics of conformational isomerization. In particular we concentrate on systems which admit phase space structures we call ‘‘reactive islands.’’ Our calculations are on a two degree of freedom model of the molecule 3-phospholene with an experimentally fit potential energy surface by Harthcock and Laane. The reactive islands (RIS) are embedded within and are part of chaotic regions of phase space. We find that the RIS are constructed from a linear stability analysis of the period 1 orbit at the transition state or approximated by a similar analysis on reactive periodic orbits. The two approaches converge as the order of the reactive periodic orbit increases. It is found that the fully constructed RIS have well defined regions of reactivity and thus mediate the process of conformational isomerization.The overlap areas of the RIS give important kinetic information such as probabilities for trapped to reactive motion, reactive to trapped motion, and primary back reaction. The implications of this work lie in precisely identifying the microscopic dynamical pathway for isomerization. The results of this work and its relation to the related work of Gray and Rice as well as its relation to contemporary work in modern dynamics is also discussed. [ABSTRACT FROM AUTHOR]

A high degree of structure and therefore order in chaos is found to exist in the detailed dynamical pathways to conformational isomerization. It is shown that this structure can be used to determine the probabilities associated with the dynamical pathways to reaction, trapping, and back reaction. An earlier publication described the mediation of the dynamics of 3-phospholene by phase space structures we called ‘‘reactive islands’’ (RIS)21. In this paper we extend the physical and mathematical properties of RIS and develop the corresponding kinetic theory. RIS theory is applied to a model of a hindered rotor and 3-phospholene. It is shown that the RIS kinetic model accurately predicts trajectory simulations of conformer population decay. Comparisons with standard RRKM theory are included. A discussion on the extension of RIS theory to quantum reactive dynamics and its relevance to laboratory experiments is also included. [ABSTRACT FROM AUTHOR]

In this paper a semiclassical quantization method is developed whose formulation and application is simple, general and accurate. We call this method semiclassical quantization by circuit counting (SQCC). SQCC is based upon evaluating the action integral along a trajectory until it undergoes a near recurrence. Several near recurrences are used to obtain a set of independent equations which can then be inverted to yield the actions for the trajectory. Once the actions are obtained a linear extrapolation is used to calculate semiclassical energies. We apply the method to two model systems: (1) three uncoupled Morse oscillators and (2) a realistic three degree of freedom model of SO2. SQCC is found to work very well for these systems. We discuss some of the advantages and disadvantages of SQCC and its application to systems with more than three coupled molecular degrees of freedom. [ABSTRACT FROM AUTHOR]

In this paper we extend the arbitrary trajectory approach to semiclassical quantization developed in an earlier paper. A numerical method is developed and tested that uses a second-order correction to extrapolate several energy eigenvalues from a single trajectory. The method is based upon finding the second-order action derivatives of the Hamiltonian. We test the scheme on a Hamiltonian previously analyzed by Swimm and Delos. We find that about 100 energy eigenvalues can be fairly accurately obtained with three reference trajectories (24 total trajectories). Strengths, weaknesses, and future applications of the method are discussed. [ABSTRACT FROM AUTHOR]

Classical resonances arising from the interaction of three nonlinearly coupled oscillators are studied from both a theoretical and numerical perspective. In particular, our study focuses on ternary classical resonances defined by n1ω1 +n2ω2 -n3ω3 =0. We discuss some of the experimental and quantum mechanical consequences of binary and ternary classical resonances (e.g., Fermi resonances and vibration–rotation coupling). Numerically we show that it is possible to construct a three-dimensional map such that ternary classical resonances can be systematically found. Theoretically, we show that canonical transformations exist between resonant and nonresonant motion. These transformations predict various structural features of the three-dimensional numerical maps which are subsequently observed in a model numerical calculation. Finally we argue that the methods and ideas presented in this paper are generic and can be used for more general systems. [ABSTRACT FROM AUTHOR]

We examine the classical limit (h→0) of the semiclassical spectral quantization method (SQ) proposed in an earlier publication. Using the classical limit analysis, equations are derived which should improve the accuracy of SQ for finite h. Our analysis is focused on problems involving coupled and uncoupled oscillator systems. Special attention is given to the situation when the unperturbed oscillators are anharmonic. Application to cases where classical resonances are present are also discussed. [ABSTRACT FROM AUTHOR]