Illinois Low Oil Research Articles

Epistatic models and pre-selection of markers improve prediction of performance in corn

In our previous papers, we demonstrated that the inclusion of epistatic interactions in marker models improved prediction for corn (Zea mays L.) grain quality traits. The utility of pre-selecting markers for epistatic models was not reported. In papers by other researchers, including epistatic effects in a model did not improve prediction efficacy for whole genome selection. The objectives of this study were therefore to evaluate the value of: (1) pre-selecting markers and interactions at different type 1 error levels to predict performance; (2) adding epistatic interactions to models including all markers, and (3) using marker-based models to predict performance of kernel weight (KWT), flowering date (FDT), and plant height (PHT). Data for KWT, FDT, PHT, and oil and protein concentrations were obtained for 500 S2 lines and their testcrosses from the crosses of Illinois high oil × Illinois low oil and Illinois high protein × Illinois low protein corn strains. Pre-selection using an epistatic model including both single-locus and two-locus interaction effects significant at the P = 0.05 level significantly increased prediction efficacy over selection including all markers and epistatic interactions. Adding all epistatic interactions to a model including all markers did not improve prediction. For most traits, prediction based on the P = 0.05 epistatic pre-selection model was nearly as effective as prediction based on phenotype, suggesting subsequent marker-based selection would be effective.

Epistatic Models Improve between Year Prediction and Prediction of Testcross Performance in Corn

In a previous paper, the utility of partial least squares as a tool for predicting performance using marker‐based models was demonstrated. Including interactions between markers in prediction models improved prediction efficacy. The objectives of this paper were to determine whether: (i) molecular marker models based on 1 yr's phenotypic data could be used to predict performance in a second year; (ii) models based on per se data would be useful in predicting testcross performance; and (iii) adding epistasis to a model would improve prediction in either case. Data for protein, oil, and starch were obtained from 500 S2 lines and their testcrosses from the crosses of Illinois High Oil (IHO) × Illinois Low Oil (ILO) and of Illinois High Protein (IHP) × Illinois Low Protein (ILP) corn (Zea mays L.) strains. Adding epistasis to a model significantly increased predictive power both between years and for testcross performance. The proportion of variability accounted for when predicting testcross performance from per se performance was lower than when predicting performance in different years. In all cases, observed vs. predicted correlations were high enough to suggest they would be useful in marker‐assisted, or marker‐based, breeding.

Epistatic Models Improve Prediction of Performance in Corn

To be useful, adding epistasis to a prediction model must increase predictive power. The objectives of this study were to determine i) using partial least squares (PLS) techniques, whether the ability to predict performance can be increased by including epistasis in a prediction model; ii) whether relaxing the probability of preselecting a marker or interaction to include in the PLS analysis from 0.001 to 0.01 to 0.05 would increase predictive power; and iii) whether the proportion of variability accounted for could be raised to a level useful in breeding. Data for protein, oil, starch, and grain yield were obtained from 500 S2 lines from the crosses of Illinois High Oil × Illinois Low Oil and of Illinois High Protein × Illinois Low Protein corn (Zea mays L.) strains. Lines per se and testcrosses were evaluated for oil, protein, and starch, and only testcrosses for grain yield. Adding epistasis to a model significantly increased predictive power, as did increasing the probability level for inclusion of significant markers and epistatic effects in the PLS analysis from 0.001 to 0.01 to 0.05. With epistasis in the model and P = 0.05, correlations of predicted and observed means were high enough to suggest they could be useful in breeding.

Epistatic Interactions in Crosses of Illinois High Oil × Illinois Low Oil and of Illinois High Protein × Illinois Low Protein Corn Strains

Epistasis has been proposed as a possible explanation for the long continued progress from selection in the Illinois long‐term corn (Zea mays L.) selection strains. From the crosses of Illinois High Oil (IHO) × Illinois Low Oil (ILO) and of Illinois High Protein (IHP) × Illinois Low Protein (ILP), 500 S2 lines were developed. Each IHO×ILO line was genotyped for 479 single nucleotide polymorphism (SNP) markers, and each IHP×ILP line was genotyped for 499 SNP markers. Per se and testcross progenies of each S2 line were evaluated for oil, protein, and starch. A large number of QTL were found to control these traits. The objective of this paper is to report the results of analysis of these crosses for two‐way epistatic interactions. More epistatic interactions were significant than expected by chance. The proportion of significant interactions that involved a marker significant in a single marker analysis (SMA) was no greater than expected by chance. The number of markers associated only with significant epistatic effects ranged from 46.3 to 72.2% of the total number of markers significant for either an interaction effect or from SMA. The number of QTL controlling a trait is much greater than will be found by analyzing for significant QTL main effects. Thus, epistasis could contribute to the long continued response to selection in the Illinois long‐term selection strains and also may help explain the continued success of commercial corn breeding.

Genetic Analysis of Corn Kernel Chemical Composition in the Random Mated 10 Generation of the Cross of Generations 70 of IHO × ILO

To identify and characterize quantitative trait loci (QTL) affecting oil, protein and starch concentration in the corn (Zea mays L.) kernel, plants from Generation 70 of the Illinois High Oil (IHO) and Illinois Low Oil (ILO) populations, previously developed by divergent selection for kernel oil concentration, were crossed. The cross was random mated 10 generations and selfed two generations to develop 500 F1RM10S2 lines. The lines per se and their testcross progenies were evaluated at three locations with two replications for 2 yr. Genotypes were evaluated using 479 SNP markers on a bulk of kernels from each line. Since the parent plants used to make the original cross were not available for genotyping, a multivariable optimization procedure was developed to estimate parental population parameters required for QTL mapping. Simple interval mapping was performed with software specially developed to account for the complex mating structure and the fact that the initial cross was made between populations. Correlations and signs of QTL effects suggest development of high oil–high starch lines would be difficult but that it should be possible to develop high oil–high protein lines. The identification of a large number of QTL (at least 40 each for oil, protein, and starch) with small effects has implications for breeding for improved corn chemical composition.

Quantitative Trait Loci for Tassel Traits in Maize

The inheritance of tassel traits in maize (Zea mays L.) is not well understood. This study was conducted to estimate the chromosomal location and magnitude of effect of major quantitative trait loci (QTL) affecting tassel branch angle (ANGLE), branches per tassel (BRANCH#), and tassel weight (TASSWT) in 200 S1 lines derived from a single F1 plant from a cross of Illinois High Oil (IHO) by Illinois Low Oil (Early Maturity) [ILO(EM)]. The restriction fragment length polymorphism (RFLP) genotypes of the 200 S1 lines were determined at 80 polymorphic loci. These lines were measured for ANGLE, BRANCH#, and TASSWT in replicated field trials during 1992 and 1993 at Urbana, IL. Composite interval mapping using selected markers as cofactors detected several QTL for each tassel trait. Six QTL located on chromosomes 2, 3, 5, 6, and 10 were significantly associated with ANGLE. They showed primarily dominant gene action and explained 43.1 and 50.7% of the phenotypic and genetic variance, respectively. Three QTL located on chromosomes 2, 4, and 7 were significantly associated with BRANCH#. They showed primarily additive gene action and explained 44.3 and 49.3% of the phenotypic and genetic variance, respectively. The QTL for BRANCH# on chromosome 7 explained 35.3% (R2) of the phenotypic variance. Seven QTL located on chromosomes 1, 2, 3, 4, and 7 were significantly associated with TASSWT. They showed primarily negative dominant gene action and explained 35.1 and 43.4% of the phenotypic and genetic variance, respectively. Most of the major QTL detected for these tassel traits were not associated with anthesis date (ANTH) in this population.

Quantitative trait locus analysis of fatty acid concentrations in maize

A study was conducted to determine the number and chromosomal location of quantitative trait loci (QTL) influencing the concentration of five fatty acids in 200 F2S1 lines derived from an Illinois High Oil (IHO) by Illinois Low Oil (Early Maturity) (ILO(EM)) cross. Restriction fragment length polymorphism (RFLP) analysis was performed on the 200 S1 lines and concentrations of palmitic (16:0), stearic (18:0), oleic (18:1), linoleic (18:2), and linolenic (18:3) acids were determined in self-pollinated kernels harvested from plants grown in replicated field trials during 1992 and 1993. A series of 74 cDNA and genomic clones were used and these revealed 80 polymorphic loci spaced, on average, 24 cM apart throughout the maize genome. Analysis of variance detected significant (p < 0.05) associations between several RFLP loci and the concentration of each fatty acid. A total of 15 RFLP loci clustered in 12 chromosomal regions were associated with the concentration of 16:0, 17 loci clustered in 10 regions were associated with the concentration of 18:0, 12 loci clustered in eight regions were associated with the concentration of 18:1 and 18:2, and 17 loci clustered in eight regions were associated with the concentration of 18:3. Multiple linear regression models consisting of four RFLP loci explained 24 and 62% of the total phenotypic and genotypic variation (R2) among the 200 F2S1 lines for 16:0, five loci explained 51 and 71% of the variation for 18:0, three loci explained 67 and 79% of the variation for 18:1, two loci explained 67 and 81% of the variation for 18:2, and seven loci explained 52 and 78% of the variation for 18:3 in these 200 F2S1 lines. The ratio of 18:1 to 18:2 was tightly interrelated as the same QTL were associated with the concentrations of 18:1 and 18:2. A quantitative trait locus that explained 63% of the phenotypic variation in the ratio of 18:1 to 18:2 is tightly linked to umc65 on chromosome 6 in the region of the linoleic acid1 locus.

Restriction fragment length polymorphism differences among Illinois long-term selection oil strains

Restriction fragment length polymorphism (RFLP) analysis was used to characterize variability in the Illinois Long-Term Selection Experiment oil strains. Considerable polymorphism was detected within each oil strain and among oil strains. Fifty-two individual plants from each of the Illinois High Oil (IHO), Illinois Low Oil (ILO), Reverse High Oil (RHO) and Reverse Low Oil (RLO) strains were sampled to determine RFLP allele/variant frequencies. Generation 90 was sampled for IHO, RHO, and RLO whereas generation 87 was sampled for ILO. Forty-nine RFLP probes distributed throughout the maize genome were used. Chi-square analysis was performed to determine if RFLP genotypes at each of the 49 RFLP loci were significantly different among strains. Oil strains that have been separated for 90 generations showed high levels of significantly-different RFLP genotypic frequencies. The comparison of ILO vs RHO gave only significant chi-square values while the comparisons of IHO vs RLO and RHO vs RLO had 11∶1 ratios of significant to non-significant chi-square values. Strains that have been separated for only 42 generations showed a lower level of significantly-different RFLP genotypic frequencies. The comparisons of IHO vs RHO and ILO vs RLO both had only a 3∶2 ratio of significant to non-significant chi-squares values. Detection of multiple RFLP alleles/variants among the oil strains was common with 59% of the RFLP loci examined exhibiting multiple variants. A number of RFLP loci in RHO (3) and RLO (11) were associated with a trend in RFLP allele/variant frequencies consistent with a response to reverse selection for oil concentration.

Lipase Activities in Scutella of Maize Lines Having Diverse Kernel Lipid Content

The maize lines, Illinois High Oil, Illinois Low Oil, and their F(1) generation contained about 18%, 0.5%, and 10%, respectively, of kernel lipids, which were present mostly in the scutella. We explored to see if the activities of gluconeogenic enzymes which appeared in postgerminative growth were proportional to the lipid content in each maize line. This proportionality was found to be valid in lipase, but the two glyoxysomal enzymes, catalase and isocitrate lyase, were the same in the three maize lines irrespective of the lipid content. The results suggest a difference in the genetic control of the gluconeogenic enzymes and a co-selection for high lipid content and high lipase activity through breeding.

Comparison of the Glyoxysomes and the Glyoxysomal Enzymes in Maize Lines with High or Low Oil Content

The developmental profile of the glyoxysomes and their component enzymes catalase, malate synthase, and isocitrate lyase were compared in the scutellum of two maize (Zea mays) lines, Illinois High Oil (IHO, approximately 20% lipid content) and Illinois Low Oil (ILO, less than 0.5% lipid content). The microbodies participate in the catabolism of the seed lipids and are responsible for leading the catabolic products (acetyl-Coenzyme A) into gluconeogenesis. The aim of this study was to determine whether changes in lipid content of the seed resulted in changes in the levels of the glyoxysomal enzymes. Enzyme activity measurements, immunological measurements (in the case of catalase), cell fractionation studies, and electron microscopic observations indicated that the IHO and ILO lines contain similar populations of glyoxysomes and exhibit similar catalase and malate synthase specific activities, despite the significant difference (40-fold) in their lipid content. Only the specific activity of isocitrate lyase was higher (2-fold higher) in the IHO seeds as compared to the ILO.

A Design III Study of Linkage Disequilibrium for Percent Oil in Maize1

The objectives of this study were 1) to estimate additive and dominance genetic variance and the average degree of dominance for percent oil in the F2 and F8 randommated generations of a cross between Illinois High Oil (IHO) and Illinois Low Oil (ILO) maize (Zea mays L.) strains using Design III and 2) to measure the effect of linkage bias on such estimates.The following results were obtained: 1) The estimate of additive genetic variance was about eight ✕ larger than that of dominance genetic variance in the F2 and about four ✕ larger in the F6; 2) The estimate of additive variance in the F8 was half that in the F2 suggesting that many loci controlling percent oil were linked in the coupling phase in the parents; 3) The estimate of dominance variance in the F6 did not differ from the F2 indicating a lack of effect of linkage on dominance variance which could be interpreted as indicating that genes with dominant action are distributed throughout the genome with map distances approximating independent inheritance or that some genes are dominant for low oil while others are dominant for high oil; 4) Estimates of the average degree of dominance were 0.508 for the F2 generation and 0.681 for the F8. Both estimates are significantly different from zero and from one, but not from each other.

Development Changes in Oil and Fatty Acid Content of Maize Strains Varying in Oil Content1

Changes in kernel and germ weight, germ percentage, oil percentage, weight of oil produced, and fatty acid distribution were studied in the maize (Zea mays L.) strains ‘Illinois High Oil’ (IHO), ‘Reverse High Oil’(RHO), ‘Illinois Low Oil’ (ILO), and ‘Reverse Low Oil’(RLO) and in a standard F1 hybrid, WF9 ✕ OH43, during the 1964 growing season. Nuclear magnetic resonance (NMR) was used for oil analyses and gas‐liquid chromatography (GLC) for determination of esterified fatty acids.Sixty‐five generations of selection for high oil resulted in: a) early and rapid development of the germ (scutellum and embryo axis), b) larger total germ weight, c) lower total endosperm and kernel weight, d) greater germ percentage, e) greater germ and kernel oil percent, and f) greater percent of total oil residing in the germ. The converse was true in the low oil selections except that total kernel weight was not changed. WF9 ✕ OH43 generally was intermediate for all characteristics, and reverse strains, although resembling the original selections, differed significantly from them for most characters.Percent of total oil was initially higher in the endosperm, but the majority of the oil was located in the germ by 20 days after pollination in the high oil strains, and by 36 days in all strains. A lower percentage of palmitic acid was found in mature than immature (24days after pollination) kernels for all strains. The percentage of oleic acid was lower and linoleic acid higher in the mature kernels and germs of WF9 ✕ OH43, ILO, and RLO.A positive correlation was found between percent oil and oleic acid percent (r = 0.947) and a negative correlation between percent oil and linoleic (r = −0.931) and palmitic (r = −.767) acid content.