Observed and predicted phenotypic effects of inbreeding in the BS13(S)C0 maize population

Inbreeding occurs at both the individual level and the population level in most plant breeding programs. Modeling systems that include inbreeding requires knowledge of how inbreeding affects genetic variance. The objectives of this work were to model the effects of inbreeding on variances of genetic effects in individuals and repartitioning of genetic variance within and among subpopulations derived from a common metapopulation. Two hundred random inbred lines were developed in the BS13(S)C0 maize population by four generations of self-pollination to study the effects of inbreeding at the individual and population level in BS13(S)C0. The 200 lines along with a set of related half-sib families were evaluated in replicated yield trials. Genetic covariances of inbred relatives were estimated for six agronomic characters. Inbreeding caused a significant change in the mean of all six traits, and an increase in the variance of dominance deviations for five of six traits demonstrating that both the mean and variance of dominance deviations are larger in inbred individuals (F = 1) than in noninbred individuals. Additionally, dominance deviations became negatively correlated with breeding values in inbred individuals. The correlation between dominance deviations and genotypic values in inbred individuals was 0.37 or less for all traits except grain yield, which had a correlation between dominance deviations and genotypic values in inbred individuals of 0.63. The average degree of dominance was found to be greater than 2 (0 is no dominance, 1 is complete dominance) for all traits except grain yield. Based on predicted effects of inbreeding on variance component structure in BS13(S)C0, additive variance for grain yield will change very little at average inbreeding coefficients less than 0.5. Other traits will lose genetic variance roughly in accord with neutral additive expectations based on estimates of additive variance in the base population. Pseudo-overdominance, combined with the high correlation between inbred dominance deviations and genotypic values may explain the lack of response to inbred-progeny recurrent selection for grain yield in the BS13(S) population. Furthermore, our results predict that genetic variance will not be exhausted in this population, a result in accord with the observed long-term maintenance of genetic variance in recurrent selection programs in the Iowa Stiff Stalk Synthetic population

Quantitative Genetics of Inbreeding in a Synthetic Maize Population

The average effects of inbreeding depression have been measured extensively in maize (Zea mays L.), but the influence of inbreeding on genetic variance has not been well studied. Two hundred random S1, S2, S3, and S4 lines were developed from the BS13(S)C0 population by single-seed descent and a set of 200 related half-sib families were developed from the S1 lines. The lines and half-sib families were evaluated in replicated yield trials for six agronomic characters. Under a purely additive model, the expected variance among inbred individuals is exactly twice the variance of noninbred individuals. The observed variance of inbred individuals in our study was 1.18 times the variance of noninbred individuals or less for five of six traits studied. By contrast, variance of dominance deviations of inbred individuals ranged from 1.6 to 3.3 times the variance of dominance deviations of noninbred individuals for five of six traits studied. A negative covariance between dominance deviations and breeding values in inbred individuals was found for all six traits. An estimator of the degree of dominance for arbitrary allele frequencies was developed. The estimated average degree of dominance in BS13(S)C0 ranged from 1.28 to 2.76, corresponding to overdominance or pseudo-overdominance. Our results suggested that some regions of linked genes have large effects on inbreeding depression in this population

The Genetic Structure of a Maize Population: The Role of Dominance

The combined effects of dominance and inbreeding on covariances between relatives are still poorly understood in maize (Zea mays L.) populations. Our objectives were to address the following questions: (i) What is the importance of dominance in a maize synthetic? (ii) How does inbreeding affect the genetic variance among individuals in a maize synthetic. (iii) How do the covariance parameters compare between populations? (iv) How does breeding design impact estimators? We estimated covariance components for inbred relatives in the maize synthetic BSCB1(R)C13. Previous estimates of covariance parameters have been used to explain the ineffectiveness of inbred progeny selection in the stiff-stalk population BS13. We found that the dominance variance was larger than the additive variance for grain yield, whereas the additive variance was larger than the dominance variance for all other traits. Negative estimates of the covariance between additive and homozygous dominance deviations were found for all traits with the exception of traits associated with reproductive maturity, suggesting a negative relationship between inbred and outbred performance. The correlation between genotypic values and breeding values was lower for grain yield than for any other trait. Our results were similar to previous results found in the stiff-stalk maize population BS13, suggesting similarity in structure among populations

Altering the fatty acid composition of Corn Belt corn through Tripsacum introgression

Breeders need sources of genes for altering the fatty acid content of oil in maize (Zea maize L.) that are not available in Corn Belt germplasm. Previously we determined lines developed from maize introgressed with genes from Tripsacum dactyloides had useful variation for fatty acid composition. We conducted this study to validate the variation, thereby showing that the trait could be transferred to Corn Belt inbreds using traditional plant breeding methods to create maize lines with altered fatty acid composition useful for an oil quality breeding program. Based on their fatty acid profiles, maize lines were selected from an open pollinated population that was introgressed with genes from Tripsacum dactyloides. These introgressed lines were both self-pollinated and backcrossed to Corn Belt lines while undergoing selection for various fatty acid compositions. The parental lines and S1 and S3 progeny from the backcrosses were compared to commercial Corn Belt hybrids and inbreds in an experiment using a randomized complete block design with two replications at two locations near Ames, Iowa. The plants were hand pollinated and hand harvested. The fatty acid compositions were analyzed by using Gas Chromatography to characterize the fatty acid methyl esters made from the oil of five individual kernels from each ear. The relative amounts of the two types of fatty acids of interest, a monounsaturated fatty acid, (oleic acid) and saturated fatty acids (palmitic and stearic acids), were greatly increased by selection breeding within the Tripsacum introgressed germplasm. New oil products with more healthful fatty acid compositions and products with reduced trans fats can be developed from these new lines

Grain composition and amino acid content in maize cultivars representing 80 years of commercial maize varieties

In order to determine how modern hybrids have impacted grain composition and amino acid content of the corn crop, we characterized a set of cultivars that were widely grown in different eras from the 1920s through 2001. Grain composition exhibited clear trends with time, with protein decreasing and starch increasing. The effects of different plant densities were examined. The grain protein content of modern hybrids responds to plant density and environment differently than the protein content of older varieties. These differences are consistent with a model in which protein content is modulated by different growth conditions. These differences may explain, in part, the mechanism by which modern hybrids maintain yield in different environments, i.e. reduction of protein content in stressful environments frees resources that are used to maintain yield. We examined the content of the nutritionally limiting essential amino acids lysine, methionine and tryptophan in grain of these cultivars. On a per tissue mass basis, the levels of these amino acids dropped with time while on a per protein basis, their levels were not significantly changed. We conclude that the development of modern hybrids has resulted in maize with reduced protein content, but the nutritional quality of this protein has not changed

USDA ARS Corn Breeding

The United States Department of AgricultureAgricultural Research Service (USDA ARS) evaluated 5,412 experimental corn research plots at the Southeast Research Farm in 2010 representing three research projects within USDA ARS: Germplasm Enhancement of Maize (GEM). The objective of the GEM project is to increase the diversity of U.S. maize germplasm utilized by producers, global end-users, and consumers. The mission is accomplished though a collaborative effort between USDA-ARS and both public and private research scientists. Genetic Analysis of Selection Response in Maize Populations. The objective of this project is to develop more efficient strategies to increase maize production. The primary emphasis is on understanding the genetics of adaptation to high plant density. Breeding High-Quality Corn for LowInput and Organic Farming Systems. The primary objective of this project is to develop germplasm for low-input and organic farming systems through conventional breeding

The PowerAtlas: a power and sample size atlas for microarray experimental design and research

BACKGROUND: Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips needed to address the multiple hypotheses with acceptable accuracy? Statistical methods exist for calculating power based upon a single hypothesis, using estimates of the variability in data from pilot studies. There is, however, a need for methods to estimate power and/or required sample sizes in situations where multiple hypotheses are being tested, such as in microarray experiments. In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies. RESULTS: To address this challenge, we have developed a Microrarray PowerAtlas [1]. The atlas enables estimation of statistical power by allowing investigators to appropriately plan studies by building upon previous studies that have similar experimental characteristics. Currently, there are sample sizes and power estimates based on 632 experiments from Gene Expression Omnibus (GEO). The PowerAtlas also permits investigators to upload their own pilot data and derive power and sample size estimates from these data. This resource will be updated regularly with new datasets from GEO and other databases such as The Nottingham Arabidopsis Stock Center (NASC). CONCLUSION: This resource provides a valuable tool for investigators who are planning efficient microarray studies and estimating required sample sizes

Molecular characterization of doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic (BSSS) maize population

Molecular characterization of a given set of maize germplasm could be useful for understanding the use of the assembled germplasm for further improvement in a breeding program, such as analyzing genetic diversity, selecting a parental line, assigning heterotic groups, creating a core set of germplasm and/or performing association analysis for traits of interest. In this study, we used single nucleotide polymorphism (SNP) markers to assess the genetic variability in a set of doubled haploid (DH) lines derived from the unselected Iowa Stiff Stalk Synthetic (BSSS) maize population, denoted as C0 (BSSS(R)C0), the seventeenth cycle of reciprocal recurrent selection in BSSS (BSSS(R)C17), denoted as C17 and the cross between BSSS(R)C0 and BSSS(R)C17 denoted as C0/C17. With the aim to explore if we have potentially lost diversity from C0 to C17 derived DH lines and observe whether useful genetic variation in C0 was left behind during the selection process since C0 could be a reservoir of genetic diversity that could be untapped using DH technology. Additionally, we quantify the contribution of the BSSS progenitors in each set of DH lines. The molecular characterization analysis confirmed the apparent separation and the loss of genetic variability from C0 to C17 through the recurrent selection process. Which was observed by the degree of differentiation between the C0_DHL versus C17_DHL groups by Wright’s F-statistics (FST). Similarly for the population structure based on principal component analysis (PCA) revealed a clear separation among groups of DH lines. Some of the progenitors had a higher genetic contribution in C0 compared with C0/C17 and C17 derived DH lines. Although genetic drift can explain most of the genetic structure genome-wide, phenotypic data provide evidence that selection has altered favorable allele frequencies in the BSSS maize population through the reciprocal recurrent selection program