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The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals’ genotype probability without significantly increasing computational demand.

Genetic linkage and association studies are empowered by proper modeling of relatedness among individuals. Such relatedness can be inferred from marker and/or pedigree information. In this study, the genetic relatedness among n inbred individuals at a particular locus is expressed as an n × n square matrix Q. The elements of Q are identity-by-descent probabilities, that is, probabilities that two individuals share an allele descended from a common ancestor. In this representation the definition of the ancestral alleles and their number remains implicit. For human inspection and further analysis, an explicit representation in terms of the ancestral allele origin and the number of alleles is desirable. To this purpose, we decompose the matrix Q by a latent class model with K classes (latent ancestral alleles). Let P be an n × K matrix with assignment probabilities of n individuals to K classes constrained such that every element is nonnegative and each row sums to 1. The problem then amounts to approximating Q by PPT, while disregarding the diagonal elements. This is not an eigenvalue problem because of the constraints on P. An efficient algorithm for calculating P is provided. We indicate the potential utility of the latent ancestral allele model. For representative locus-specific Q matrices constructed for a set of maize inbreds, the proposed model recovered the known ancestry.

The development of single nucleotide polymorphism (SNP) markers in maize offers the opportunity to utilize DNA markers in many new areas of population genetics, gene discovery, plant breeding and germplasm identification. However, the steps from sequencing and SNP discovery to SNP marker design and validation are lengthy and expensive. Access to a set of validated SNP markers is a significant advantage to maize researchers who wish to apply SNPs in scientific inquiry. We mined 1,088 loci sequenced across 60 public inbreds that have been used in maize breeding in North America and Europe. We then selected 640 SNPs using generalized marker design criteria that enable utilization with several SNP chemistries. While SNPs were found on average every 43 bases in 1,088 maize gene sequences, SNPs that were amenable to marker design were found on average every 623 bases; representing only 7% of the total SNPs discovered. We also describe the development of a 768 marker multiplex assay for use on the Illumina® BeadArray™ platform. SNP markers were mapped on the IBM2 intermated B73 × Mo17 high resolution genetic map using either the IBM2 segregating population, or segregation in multiple parent-progeny triplets. A high degree of colinearity was found with the genetic nested association map. For each SNP presented we give information on map location, polymorphism rates in different heterotic groups and performance on the Illumina® platform.

Allelic differences in expression are important genetic factors contributing to quantitative trait variation in various organisms. However, the extent of genome-wide allele-specific expression by different modes of gene regulation has not been well characterized in plants. In this study we developed a new methodology for allele-specific expression analysis by applying Massively Parallel Signature Sequencing (MPSS™), an open ended and sequencing based mRNA profiling technology. This methodology enabled a genome-wide evaluation of cis- and trans-effects on allelic expression in six meristem stages of the maize hybrid. Summarization of data from nearly 400 pairs of MPSS allelic signature tags showed that 60% of the genes in the hybrid meristems exhibited differential allelic expression. Because both alleles are subjected to the same trans-acting factors in the hybrid, the data suggest the abundance of cis-regulatory differences in the genome. Comparing the same allele expressed in the hybrid versus its inbred parents showed that 40% of the genes were differentially expressed, suggesting different trans-acting effects present in different genotypes. Such trans-acting effects may result in gene expression in the hybrid different from allelic additive expression. With this approach we quantified gene expression in the hybrid relative to its inbred parents at the allele-specific level. As compared to measuring total transcript levels, this study provides a new level of understanding of different modes of gene regulation in the hybrid and the molecular basis of heterosis.

Surveys of pedigree usage indicate that breeding programs can generate genetic diversity in time. There are also concerns that genetic diversity is being lost. Previous studies of pedigree usage in U.S. maize (Zea mays L.) production have reviewed usage of publicly bred inbred lines. However, proprietary inbred lines were already contributing over 90% of U.S. maize production by 1985. This chronological study of germplasm usage compliments previous studies of genetic diversity in U.S. maize production by reporting the pedigree backgrounds of 68 proprietary, widely used maize hybrids released by Pioneer Hi-Bred International during the period 1930 to 1999. Objectives are to identify founder sources for the hybrids and to reveal changes in founder contributions through time. We also compare founder usage with pedigrees of widely used U.S. public inbred lines to measure the extent of their reliance on common germplasm, backgrounds. Pedigrees of the hybrids collectively traced to at least 61 founders. Several founders of the hybrids had complex pedigrees. Founder backgrounds of the hybrids could be traced to at least 22 landraces with additional contributions from other populations or landraces. Public lines used for comparison traced to 14 founders. Nine founders of the public lines were common in the era hybrids; five were unique to the public lines. Differences in founder contributions were evident for the era hybrids and the public lines. Significant contributions from both the private and public sectors were evident in the pedigrees of the era hybrids. Diversity in time was evident. Hybrids tended to associate by decade of initial release. Most new founder contributions occurred in the 1940s (35%), 1960s (36%), and 1980s (20%). Breeding networks have allowed germplasm that was once exotic to the central Corn Belt to contribute improved productivity in that region.

Microsatellites are important tools for plant breeding, genetics, and evolution, but few studies have analyzed their mutation pattern in plants. In this study, we estimated the mutation rate for 142 microsatellite loci in maize (Zea mays subsp. mays) in two different experiments of mutation accumulation. The mutation rate per generation was estimated to be 7.7 x 10(-4) for microsatellites with dinucleotide repeat motifs, with a 95% confidence interval from 5.2 x 10(-4) to 1.1 x 10(-3). For microsatellites with repeat motifs of more than 2 bp in length, no mutations were detected; so we could only estimate the upper 95% confidence limit of 5.1 x 10(-5) for the mutation rate. For dinucleotide repeat microsatellites, we also determined that the variance of change in the number of repeats (sigma(m)2) is 3.2. We sequenced 55 of the 73 observed mutations, and all mutations proved to be changes in the number of repeats in the microsatellite or in mononucleotide tracts flanking the microsatellite. There is a higher probability to mutate to an allele of larger size. There is heterogeneity in the mutation rate among dinucleotide microsatellites and a positive correlation between the number of repeats in the progenitor allele and the mutation rate. The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation.

Recently, a new type of molecular marker has been developed that is based on the presence or absence of the miniature inverted repeat transposable element (MITE) family Heartbreaker ( Hbr) in the maize genome. These so-called Hbr markers have been shown to be stable, highly polymorphic, easily mapped, and evenly distributed throughout the maize genome. In this work, we used Hbr-derived markers for genetic characterization of a set of maize inbred lines belonging to Stiff Stalk (SS) and Non-Stiff Stalk (NSS) heterotic groups. In total, 111 markers were evaluated across 62 SS and NSS lines. Seventy six markers (68%) were shared between the two groups, and 25 of the common markers occurred at fairly low frequency (/=0.20). Only two markers (3%) were monomorphic in all samples. Although DNA sequencing indicated that 5.5% of same-sized DNA fragments were non-homologous, this result did not affect the cluster analyses (i.e., relationships obtained from the Hbr data were congruent with those derived from pedigree information). Distance matrices generated from Hbr markers were significantly correlated ( p0.001) with those obtained from pedigree ( r=0.782), RFLPs ( r=0.747), and SSRs ( r=0.719). Overall, these results indicated that Hbr markers could be used in conjunction with other molecular markers for genotyping and relationship studies of related maize inbred lines.

Yield prediction across a target production zone with varying strategies of agronomic practices has been a challenging problem to plant breeders when testing new genotypes for release. This study focused on comparing the importance of a new bioclimatic index called biological windows and six other traditional environmental indices as predictor variables of maize yields across sites (farmers' fields) and years, using a simple linear regression model. The yield data were collected for six hybrids evaluated in strip tests at 57 to 186 sites throughout Iowa during 1987-1994. The biological windows index was based on the Newhall Simulation Model and estimated the number of days the soil was moist and above 5°C. The environmental indices were July precipitation, temperature, the product of July precipitation and temperature, and the equivalent values for August. Because the actual values for the indices were not recorded at each site, all the indices were estimated for each site as the weighted averages of the data from 112 Iowa weather stations. Across years and within the Iowa sites, the mean percentiles of R-square distributions showed that biological windows had less predictive value for maize yields than the more traditional indicators such as August precipitation and temperature. For all indices, across years and within sites had much greater mean R-squares than across sites and within years, which had very low predictive values. For predicting yield across years within sites, there appeared to be an advantage in using August precipitation or the product of August precipitation and temperature over the five other indices. The R-square values for these two indices were at least 0.60 in 80% of the test sites for five hybrids.

theoretical response of yield in self-pollinated crops. Other researchers have addressed this relationship with Determining the appropriate number of lines to retain across generrespect to maize (Baker and Curnow, 1969; Rawlings, ations during inbred line development in maize (Zea mays L.) is interest during line development is performance of testcross progeny, Using a specific genetic model assuming additivity genetic information on lines per se adds to basic understanding of the within and among loci (no dominance, no epistasis) and genetic response of maize to inbreeding and selection. The objective of no linkage, Baker and Curnow (1969) simulated effects this research was to compare genetic responses of families per se to of population size on progress from selection in maize. varying selection intensities across early generations of selfing in In this simulation study, selection was aimed at improvmaize. A FORTRAN program simulating a stochastic genetic model ing the composite population as a source of inbred lines. with 30, 40, and 30% additive, dominant, and over-dominant loci, Rawlings (1979) discussed choices of effective popularespectively, and a random environmental effect was used to compare tion size considering short- and long-term objectives in varying combinations of selection intensities across generations. In the recurrent selection programs from the standpoint of simulation, individual plants were evaluated on the basis of testcross progeny performance using multiple testers and environments. Indi- gene fixation, maintenance of genetic variation, and vidual plants corresponding to top performing testcross progenies linkage equilibrium, and gave formulas for calculating were selected as parents for successive generations. Within each gener- appropriate population sizes and selection intensities. ation, phenotypic and genetic means of families per se increased with From a survey of U.S. maize breeders, Bauman (1981) increased selection intensities. Response to selection in any given found that, on average, U.S. maize breeders started with generation was not dependent on selection intensity used in the previ- approximately 500 S1 families and by the S4 generation, ous generation. Percent homozygosity and frequency of superior al- only 40 were retained. Bauman pointed out that breedleles increased as selection pressure intensified. Few original plants ers discarded 64% of the families in S1 generation based contributed to retained families with only approximately 5% of S0 on visual selection, indicating that both visual selection plants appearing in pedigrees of selected S4 families. Retaining few but larger families resulted in increased genetic values of families per and the breeder’s experience were important in selecse, compared with saving a large number of smaller families, even tion. Using procedures outlined by Robson et al. (1967), though selection was based on testcross performance. Johnson (1989) calculated the probability of correctly identifying S3 progenies on the basis of S2 testcross performance and found that critical decisions on allocation

An approach to selection is proposed that is based on the probabilities that a test cultivar outperforms a check by more than an amount d in a future environment. The function that gives these probabilities for all possible values of d is called the reliability function. When d=0, the value of the reliability function is the probability that the test cultivar outperforms the check. The method is illustrated using data from on-farm maize (Zea mays L.) strip test trials grown cooperatively by Pioneer Hi-bred International and farmers. Results indicate that reliability functions are useful for evaluating how test cultivars perform relative to a check across a range of environments since the location, slope and shape of the reliability function may be used to describe a test cultivar's performance, similarity to the check and stability, and identify environments where the test cultivar has performance problems.

Previous methods to differentiate U.S. maize hybrids using biochemical data have been criticized on the basis that the genome has been inadequately sampled. The objective of this study was to utilize an additional set of highly polymorphic genetic markers (restriction fragment length polymorphisms; RFLPs) to establish the degree to which these data discriminate among 78 elite maize (Zea mays L.) U.S. hybrids selected with a bias toward including hybrid pairs previously undifferentiated by biochemical data. Thirty-eight probes revealed 288 RFLP variants across all hybrids. RFLP and biochemical data clustered most hybrids into similar groupings. For those hybrids of known pedigree, distances between hybrids on the basis of pedigree showed a correlation of r = 0.91 with RFLP distances. Where available, field performance data gave identical groupings of hybrids as were shown by RFLP data. These data show that RFLPs can provide a practical means of differentiating hybrids.

Eighty DNA Restriction Fragment Length Polymorphism (RFLP) clones were used as probes to profile 47 hybrids of maize (Zea mays L.) that are of widespread usage in France and 49 hybrids that are either in common usage or are new releases in the U.S. The objectives were to 1) investigate the degree to which RFLPs provide unique characterization of hybrids; 2) show associations among hybrids using both cluster and principal coordinate analyses; 3) measure the ability of RFLPs to show associations among hybrids that reflect those to be expected on the basis of pedigree; and 4) compare the patterns and extent of genetic diversity among French hybrids with that found among a set of widely used U.S. hybrids. RFLPs showed all French hybrids to have different profiles, however, 3 hybrids were very similar with more than 90% of their profiles in common. Twenty-seven U.S. hybrids showed this level of similarity with one or more U.S. hybrids. High correlations (r=0.93, 0.94) were found for pedigree distance versus RFLP distance between pairs of French and of French and U.S. hybrids, respectively. Similar levels of correspondence for rank correlations between RFLP and pedigree data were also found. Similar groupings of hybrids were shown by two cluster analysis methods and by principal coordinate analysis. Inclusion of hybrids in cluster groupings was supported by observation of raw distance data for selected hybrids and their nearest neighbors. Most hectarage in France is planted to hybrids that fall within 2 related groups of germplasm on the basis of RFLP data. Minimum distance standards could promote breeders to surmount the challenge of introducing elite yet diverse germplasm into agriculture.

Two-dimensional electrophoresis and fluorography of [35S]methionine labeled maize germinated embryo proteins were performed at Cold Spring Harbor Laboratory. Fluorographs of 63 gels representing 37 inbred lines were subsequently scanned and spot-detected at Protein and DNA Imageware Systems (Huntington Station, NY). The digitized images were then matched with the aid of PDQUEST-II computer software. Over 1500 different protein spots were included in the resulting dataset. The optical density data were normalized to parts per million, then transformed to their natural logarithms. Analyses of variance were performed on each spot in order to select for further study those spots with most of their variation partitioned among inbred lines rather than within inbred lines. Using this method of spot selection, over 100 protein spots were included in the set of spots which display significant differences among inbred lines of maize.

Heterosis, or hybrid vigor, has been widely exploited in plant breeding for many decades, but the molecular mechanisms underlying the phenomenon remain unknown. In this study, we applied genome-wide transcript profiling to gain a global picture of the ways in which a large proportion of genes are expressed in the immature ear tissues of a series of 16 maize hybrids that vary in their degree of heterosis. Key observations include: (1) the proportion of allelic additively expressed genes is positively associated with hybrid yield and heterosis; (2) the proportion of genes that exhibit a bias towards the expression level of the paternal parent is negatively correlated with hybrid yield and heterosis; and (3) there is no correlation between the over- or under-expression of specific genes in maize hybrids with either yield or heterosis. The relationship of the expression patterns with hybrid performance is substantiated by analysis of a genetically improved modern hybrid (Pioneer® hybrid 3394) versus a less improved older hybrid (Pioneer® hybrid 3306) grown at different levels of plant density stress. The proportion of allelic additively expressed genes is positively associated with the modern high yielding hybrid, heterosis and high yielding environments, whereas the converse is true for the paternally biased gene expression. The dynamic changes of gene expression in hybrids responding to genotype and environment may result from differential regulation of the two parental alleles. Our findings suggest that differential allele regulation may play an important role in hybrid yield or heterosis, and provide a new insight to the molecular understanding of the underlying mechanisms of heterosis.

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.

Allelic expression variation of nonimprinted autosomal genes has recently been uncovered in mouse hybrids and humans. The allelic expression variation is attributed to differences in noncoding DNA sequences and does not involve epigenetic regulation or gene imprinting. This expression variation is suggested to play important roles in determining phenotypic diversity. Virtually nothing is known about such allele-specific expression variation in a hybrid plant where two alleles are compared in the same genetic context. We examined parental transcript accumulation in maize (Zea mays) hybrids using allele-specific RT-PCR analysis. Among 15 genes analyzed, 11 showed differences at the RNA level, ranging from unequal expression of the two alleles (biallelic) to expression of a single allele (monoallelic). Maternal or paternal transmission had little effect on the allele-specific transcript ratio of nearly all genes analyzed, suggesting that parent-of-origin effect was minimal. We analyzed the allelic difference in genetically contrasting hybrids and hybrids under high planting density and drought stress. Whereas a genetically improved modern hybrid expressed both alleles, a less improved old hybrid frequently showed mono-allelic expression. Furthermore, the two alleles in the hybrid responded differentially to abiotic stresses. The results of allele-specific regulation in different tissues in responding to environment and stress suggest an unequivalent function of the parental alleles in the hybrid, which may have an impact on heterosis.

The recurrent intermating of F2 individuals for some number of generations followed by several generations of inbreeding produces an intermated recombinant inbred (IRI) population. Such populations are currently being developed in the plant-breeding community because linkage associations present in an F2 population are broken down and a population of fixed inbred lines is also created. The increased levels of recombination enable higher-resolution mapping in IRI populations relative to F2 populations. Herein we derive relationships, under several limiting assumptions, for determining the expected recombination fraction in IRI populations from the crossover rate per meiosis. These relationships are applicable to situations where the inbreeding component of IRI population development is by either self-fertilization or full-sib mating. Additionally, we show that the derived equations can be solved for the crossover rate per meiosis if the recombination fraction is known for the IRI population. Thus, the observed recombination fraction in any IRI population can be expressed on an F2 basis. The implications of this work on the expansion of genetic maps in IRI populations and limits for detecting linkage between markers are also considered.

Publisher Summary Descriptive names given to landraces or cultivated varieties illustrate the practical necessity for farmers to identify sources of seed of proved performance. In many cases, processors and end-use consumers also want to know varietal identity. Usage of protein and DNA descriptors has propelled the science of both human and cultivated plant identification into the mainstream of peer-reviewed and widely accepted science. Morphological descriptions can provide unique identification of cultivated varieties. Morphologies reflect not only the genetic constitution of the cultivar, but also the interaction of the genotype with the environment (G x E) within which it is expressed. Proteins and DNA can be used to provide varietal profiles. They are in popular usage because the variation for these markers is ubiquitous and this variation can be understood in genetic terms. Most advances in varietal descriptions will involve the use of DNA as a descriptor. Some technical developments coming from other genome mapping and sequencing projects will also come to bear on cultivar fingerprinting in the future. Intense impetus to these efforts comes from the desirability to use genetic marker data in applied plant-breeding programs.

The premise that is explored in this paper is that in some cases, in order to make progress in the design of molecular breeding strategies for complex traits, we will need a theoretical framework for quantitative genetics that is grounded in the concept of gene-networks. We seek to develop a gene-to-phenotype (G→P) modelling framework for quantitative genetics that explicitly deals with the context-dependent gene effects that are attributed to genes functioning within networks, i.e. epistasis, gene × environment interactions, and pleiotropy. The E(NK) model is discussed as a starting point for building such a theoretical framework for complex trait genetics. Applying this framework to a combination of theoretical and empirical G→P models, we find that although many of the context-dependent effects of genetic variation on phenotypic variation can reduce the rate of genetic progress from breeding, it is possible to design molecular breeding strategies for complex traits that on average will outperform phenotypic selection. However, to realise these potential advantages, empirical G→P models of the traits will need to take into consideration the context-dependent effects that are a consequence of epistasis, gene × environment interactions, and pleiotropy. Some promising G→P modelling directions are discussed.

Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2–8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.

The statistical properties associated with molecular markers are important when used to characterize germplasm. Evaluation of these properties are necessary for informed selection of one marker system over another. Five different molecular marker systems, Amplified Fragment Length Polymorphism (AFLPs), Arbitrary Primed Polymerase Chain Reaction (AP-PCR), Random Amplified Polymorphic DNA (RAPDs), Restriction Fragment Length Polymorphism (RFLPs), and Isozymes were used to evaluate 39 elite corn belt inbreds. Each system was characterized for fragment frequency distribution, and band correlation distribution as a measure of independence. A regression model estimating resolution and rate of information addition was constructed using the sampling variance. All marker systems were evaluated according to this model. The model facilitated genetic relationships among the inbreds to be compared at equivalent performance level among all marker systems. Four performance levels resulted in 10 comparisons. Pairwise test of significance were conducted using t tests where the null-distributions were obtained by the bootstrap procedure. The maker system were ranked, assisting breeders in selecting marker systems for germplasm organization.

The sampling method was applied to a data-set generated by RFLP molecular marker analysis, representing 37 Zea maize cultivars. A total of 251 enzyme probe-combinations were used yielding a total of 1,205 scores per genotype. Genetic distance was calculated among all 37 entries from subsets of arbitrary and increasing sample size. Each score entry in the subset was selected at random from all possible scores with replacement following each selection. The variance for genetic distance was calculated among all subsets of equal size for all possible cultivar pairs. The pooled pair variance was plotted and compared to random simulation models. Additional comparisons were made contrasting closely vs. distantly related cultivars.

Phenotypic and genotypic correlations were examined for four traits in seven populations of maize (Zea mays L.) undergoing recurrent selection. Correlations among grain yield and percentage of grain moisture, root lodging, and stalk lodging were low (|r| 0.5). Two indices, one that used heritabilities as index weights and one that used relative economic weights (base index) as index weights, were compared with the Smith-Hazel index (optimim index). Relative efficiencies of the two indices, in terms of predicted gains for the individual traits and the composite trait, compared with the Smith-Hazel index, were high. The use of an index in which heritabilities were used as index weights was recommended because:1) the heritabilities were the same as the optimum weights when the traits were uncorrelated, and for the data examined the correlations were low; and 2) heritabilities were computed in routine data analyses and were available at no additional cost.

Alcohol soluble seed storage proteins (zeins and alcohol soluble glutelins) of maize (Zea mays L.) were separated by reversed-phase high-performance liquid chromatography (RP-HPLC). The objectives were to assess the reproducibility of chromatographic profiles using seed of inbred lines that had been produced in different locations and years. Reproducible differences between sources were seen but these were restricted to proteins that contributed 2% or less to an inbred profile. The majority of variation (93% for peak percent area; 99.8% for elution time) was between inbreds. RP-HPLC can therefore provide distinctive phenotypic profiles that are largely characteristic of genotype. Such qualitative and quantitative data will be valuable for studies of taxonomy, evolution, genetics, and germplasm identification.

Improvements in maize (Zea mays L.) yields have been due to improvements in production inputs as well as to cultivars that have improved performance at low levels of inputs and the ability to respond to high levels of inputs used on today's farms. The objectives of this study were to estimate genetic rates of gain and inbreeding depression by evaluating populations representative of each of seven eras of maize breeding. Inbred lines representative of each of the six decades (eras) from 1930 to 1980 were intermated to produce six era populations. A seventh, pre-1930 era, was represented by the open-pollinated cultivars (OP) ‘Reids Yellow Dent’ and ‘Lancaster Sure Crop’. These eight entries along with three check populations were evaluated in six Iowa environments. In addition, to assess changes in the rates of inbreeding depression, S1 bulk populations of the six era populations and OP and S2 bulks of the three check populations were also evaluated. The average genetic rate of gain for grain yield was 0.52 ± 0.04 Mg ha-1 era-1 when OP was included in the analysis. By assuming 10 yr per era, the yearly genetic rate of gain was 0.052 ± 0.004 Mg ha-1. The rates of genetic gain for percentage of stalk lodging and grain moisture at harvest were −5.1 ± 0.5% era-1 and 0.44 ± 0.09% era-1, respectively. The rate of inbreeding depression for yield increased steadily over eras, and the rate of inbreeding depression for Era 6 was double that for the OP. However, inbreeding depression as a percentage of the So mean showed no directional changes and was similar for all eras. These results indicate that breeders have been effective at selecting lines and hybrids with higher yields and resistance to lodging and the ability to produce higher yields under stress conditions. The increased rates of inbreeding depression for the more recent eras coupled with the increased performance of the S0 and S1 populations suggest that favorable allele frequencies were initially below 0.5 and have been increasing and]or that the more recent era populations are segregating at more loci

Our objective was to determine if changes in genetic variance had occurred after recurrent selection primarily for grain yield in two maize (Zea mays L.) selection programs originating from «Iowa Stiff Stalk Synthetic» (BSSSSCO)

Separations of kafirin and alcohol soluble glutelin proteins by reversed-phase high-performance liquid chromatography (RP-HPLC) from 7 inbreds and one hybrid of sorghum [Sorghum bicolor (L.) Moench] and one source of Johnsongrass [Sorghum halapense (L.) Pers.] were compared. Objectives were to assess the stability of protein profiles for seed sources produced at different locations and in different environments to examine the potential of RP-HPLC to provide genotypic profiles for sorghum. Analyses of variance data showed that levels of variation due to environments and locations were small; the majority of variation (93%) was among genotypes. Associations among inbreds revealed by multivariate and cluster analysis showed similarity with those that would be expected on the basis of pedigree. A chi-square analysis showed no deviation in the hybrid profile from the expected 2∶1 ratio of peaks from the female and male inbred parents, respectively. Improvements in the ability to correctly assign common peaks are necessary before associations among numerous sorghum genotypes can be reliably demonstrated by analysis of data from reversed-phase high-performance liquid chromatography (RP-HPLC).

Variance component estimates were obtained in a North Carolina Design I experiment for several traits in pickling cucumber (Cucumis sativus L.) for a simulated once-over mechanical harvest. The reference population was random-mating and derived from 18 inbred lines obtained from several U.S. breeding programs. Environments sampled were the spring and fall of a single year. Data indicated most of the genetic variance was additive for all traits except fruit color. Evidence for relatively large genotype by environment interaction variances were found for number of fruit, length to diameter (L/D) ratio, and fruit firmness. Heritabilities, based on full-sib families grown in 2 replications in each of 2 seasons, for dollar value and number of fruit, were .19 and .17 respectively. Genotypic and phenotypic correlations for number of fruit and dollar value were high indicating selection for increased number of fruit would be effective in increasing crop value.

Experiments conducted in the greenhouse and in the field indicated that plants produced from seedlings of Cucumis sativus L. which displayed their cotyledons in an upward position grew faster than plants which displayed their cotyledons in a downward position. Cotyledon angle was not a function of seed size nor seedling weight at 10 days after planting. An increase in plant height, node number, and fresh weight at later growth stages was associated with an upward cotyledon angle and persisted until time of harvest. Anthesis tended to occur later in plants having a downward cotyledon angle. The number of pistillate flowers was greater in plants with an upward cotyledon angle compared to those with a downward cotyledon angle. Differences in yield (fruit number) were not associated with cotyledon angle.

Three harvest methods and 3 plot sizes for estimating yields in pickling cucumbers (Cucumis sativus L.) were examined. The correlation between dollar values for a simulated once-over harvest and successive harvest were low (r < .16). Correlation between once-over harvest value and fruit number was .84, while correlation between once-over harvest value and mature fruit number was only .36. The correlation of .84 was high enough to warrant use of fruit number as a primary trait in selection for increased value. Use of fruit number as an estimate of yield would eliminate the grading and weighing processes needed to compute value. An efficient plot size for estimating mean differences between lines was 3.6m2.